Genome Analysis Wiki - User contributions [en]

http://genome.sph.umich.edu/w/api.php?action=feedcontributions&feedformat=atom&user=Yancylo Genome Analysis Wiki - User contributions [en] 2026-09-24T14:41:25Z User contributions MediaWiki 1.43.1 http://genome.sph.umich.edu/w/index.php?title=UMAKE-glfSingle&diff=9380 UMAKE-glfSingle 2014-01-22T16:32:25Z

<p>Yancylo: /* Ingredients */</p> <hr /> <div>This is a modification of UMAKE to incorporate an individual-based variant caller in the pipeline.<br /> <br /> The idea is to use glfSingle to generate sample-specific VCF after pileup, and then replace the glfMultiples step by a merging step. The merging generates a population VCF that looks the same as what would have been the glfMultiples output. Subsequent filtering and imputation steps can follow as usual.<br /> <br /> ==Ingredients==<br /> *Index file<br /> **same as original UMAKE index<br /> **An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.index<br /> *Configuration file<br /> **same as original UMAKE conf<br /> **An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf<br /> **Note that the glfSingle and merging steps are included by enabling these two steps:<br /> RUN_PILEUP = TRUE # create GLF file from BAM then individual VCF using glfSingle (sorry, you have to redo the pileups)<br /> RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls, population VCF by merging the glfSingle outputs<br /> <br /> *Perl script for generating Makefile<br /> **Found at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl<br /> **It is modified from umake.pl to use glfSingle and merge_glfS_vcf.py (for merging across single-sample VCF)<br /> ***These two programs are available at /net/wonderland/home/yancylo/bin/umake-glfSingle<br /> **To generate the Makefile corresponding to this new pipeline flow, do:<br /> perl /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl --conf /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf<br /> <br /> ==Customization==<br /> *To change paths to glfSingle and merge_glfS_vcf.py, go to the following lines of umake-glfSingle.pl:<br /> **line 1000 - my $cmd = "python [your-path]/merge_glfS_vcf.py --file-list $glfAlias --chr $chr --outfile $vcf > $vcf.log";<br /> **line 1073 - $cmd .= "\n\t".&getMosixCmd("[your-path]/glfSingle -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference > $smVcf.log");<br /> *To apply the uniform Ts/Tv model to glfSingle, go to the following line of umake-glfSingle.pl and make the changes in bold:<br /> **line 1073 - $cmd .= "\n\t".&getMosixCmd("/net/wonderland/home/yancylo/bin/umake-glfSingle/'''glfSingle_ut''' -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference '''--uniformTsTv''' > $smVcf.log");<br /> *To delete single-sample VCFs after merging, add the --d option to line 1000 (do python merge_glfS_vcf.py to view option parameters)<br /> <br /> ==Remarks==<br /> *The --reference option should be enabled for glfSingle, such that it calls the homozygous reference genotypes per sample. This is necessary to distinguish between homref and missing genotypes during merging.<br /> *The merging program combines across individual-sample VCFs in small chunks of positions, hence it does NOT create a memory issue even when merging across large sample sizes and big regions.<br /> *One potential concern of this pipeline is the number and size of additional files, since each sample now has its own set of VCFs (~2Gb for chr20 per sample).<br /> <br /> ==Contact==<br /> Please contact Yancy if you have any questions.</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=UMAKE-glfSingle&diff=9379 UMAKE-glfSingle 2014-01-22T16:30:05Z

<p>Yancylo: /* Customization */</p> <hr /> <div>This is a modification of UMAKE to incorporate an individual-based variant caller in the pipeline.<br /> <br /> The idea is to use glfSingle to generate sample-specific VCF after pileup, and then replace the glfMultiples step by a merging step. The merging generates a population VCF that looks the same as what would have been the glfMultiples output. Subsequent filtering and imputation steps can follow as usual.<br /> <br /> ==Ingredients==<br /> *Index file<br /> **same as original UMAKE index<br /> **An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.index<br /> *Configuration file<br /> **same as original UMAKE conf<br /> **An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf<br /> **Note that the glfSingle and merging steps are included by enabling these two steps:<br /> RUN_PILEUP = TRUE # create GLF file from BAM then individual VCF using glfSingle<br /> RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls, population VCF by merging the glfSingle outputs<br /> <br /> *Perl script for generating Makefile<br /> **Found at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl<br /> **It is modified from umake.pl to use glfSingle and merge_glfS_vcf.py (for merging across single-sample VCF)<br /> ***These two programs are available at /net/wonderland/home/yancylo/bin/umake-glfSingle<br /> **To generate the Makefile corresponding to this new pipeline flow, do:<br /> perl /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl --conf /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf<br /> <br /> ==Customization==<br /> *To change paths to glfSingle and merge_glfS_vcf.py, go to the following lines of umake-glfSingle.pl:<br /> **line 1000 - my $cmd = "python [your-path]/merge_glfS_vcf.py --file-list $glfAlias --chr $chr --outfile $vcf > $vcf.log";<br /> **line 1073 - $cmd .= "\n\t".&getMosixCmd("[your-path]/glfSingle -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference > $smVcf.log");<br /> *To apply the uniform Ts/Tv model to glfSingle, go to the following line of umake-glfSingle.pl and make the changes in bold:<br /> **line 1073 - $cmd .= "\n\t".&getMosixCmd("/net/wonderland/home/yancylo/bin/umake-glfSingle/'''glfSingle_ut''' -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference '''--uniformTsTv''' > $smVcf.log");<br /> *To delete single-sample VCFs after merging, add the --d option to line 1000 (do python merge_glfS_vcf.py to view option parameters)<br /> <br /> ==Remarks==<br /> *The --reference option should be enabled for glfSingle, such that it calls the homozygous reference genotypes per sample. This is necessary to distinguish between homref and missing genotypes during merging.<br /> *The merging program combines across individual-sample VCFs in small chunks of positions, hence it does NOT create a memory issue even when merging across large sample sizes and big regions.<br /> *One potential concern of this pipeline is the number and size of additional files, since each sample now has its own set of VCFs (~2Gb for chr20 per sample).<br /> <br /> ==Contact==<br /> Please contact Yancy if you have any questions.</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=UMAKE-glfSingle&diff=9378 UMAKE-glfSingle 2014-01-22T16:29:41Z

<p>Yancylo: </p> <hr /> <div>This is a modification of UMAKE to incorporate an individual-based variant caller in the pipeline.<br /> <br /> The idea is to use glfSingle to generate sample-specific VCF after pileup, and then replace the glfMultiples step by a merging step. The merging generates a population VCF that looks the same as what would have been the glfMultiples output. Subsequent filtering and imputation steps can follow as usual.<br /> <br /> ==Ingredients==<br /> *Index file<br /> **same as original UMAKE index<br /> **An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.index<br /> *Configuration file<br /> **same as original UMAKE conf<br /> **An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf<br /> **Note that the glfSingle and merging steps are included by enabling these two steps:<br /> RUN_PILEUP = TRUE # create GLF file from BAM then individual VCF using glfSingle<br /> RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls, population VCF by merging the glfSingle outputs<br /> <br /> *Perl script for generating Makefile<br /> **Found at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl<br /> **It is modified from umake.pl to use glfSingle and merge_glfS_vcf.py (for merging across single-sample VCF)<br /> ***These two programs are available at /net/wonderland/home/yancylo/bin/umake-glfSingle<br /> **To generate the Makefile corresponding to this new pipeline flow, do:<br /> perl /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl --conf /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf<br /> <br /> ==Customization==<br /> *To change paths to glfSingle and merge_glfS_vcf.py, go to the following lines of umake-glfSingle.pl:<br /> **line 1000 - my $cmd = "python [your-path]/merge_glfS_vcf.py --file-list $glfAlias --chr $chr --outfile $vcf > $vcf.log";<br /> **line 1073 - $cmd .= "\n\t".&getMosixCmd("[your-path]/glfSingle -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference > $smVcf.log");<br /> *To apply the uniform Ts/Tv model to glfSingle, go to the following line of umake-glfSingle.pl and make the changes in bold:<br /> **line 1073 - $cmd .= "\n\t".&getMosixCmd("/net/wonderland/home/yancylo/bin/umake-glfSingle/'''glfSingle_ut''' -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference '''--uniformTsTv''' > $smVcf.log");<br /> *To delete single-sample VCFs after merging, add the --d option to line 1000<br /> <br /> ==Remarks==<br /> *The --reference option should be enabled for glfSingle, such that it calls the homozygous reference genotypes per sample. This is necessary to distinguish between homref and missing genotypes during merging.<br /> *The merging program combines across individual-sample VCFs in small chunks of positions, hence it does NOT create a memory issue even when merging across large sample sizes and big regions.<br /> *One potential concern of this pipeline is the number and size of additional files, since each sample now has its own set of VCFs (~2Gb for chr20 per sample).<br /> <br /> ==Contact==<br /> Please contact Yancy if you have any questions.</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=UMAKE-glfSingle&diff=9366 UMAKE-glfSingle 2014-01-15T21:51:43Z

<p>Yancylo: /* Ingredients */</p> <hr /> <div>This is a modification of UMAKE to incorporate an individual-based variant caller in the pipeline.<br /> <br /> The idea is to use glfSingle to generate sample-specific VCF after pileup, and then replace the glfMultiples step by a merging step. The merging generates a population VCF that looks the same as what would have been the glfMultiples output. Subsequent filtering and imputation steps can follow as usual.<br /> <br /> ==Ingredients==<br /> *Index file<br /> **same as original UMAKE index<br /> **An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.index<br /> *Configuration file<br /> **same as original UMAKE conf<br /> **An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf<br /> **Note that the glfSingle and merging steps are included by enabling these two steps:<br /> RUN_PILEUP = TRUE # create GLF file from BAM then individual VCF using glfSingle<br /> RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls, population VCF by merging the glfSingle outputs<br /> <br /> *Perl script for generating Makefile<br /> **Found at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl<br /> **It is modified from umake.pl to use glfSingle and merge_glfS_vcf.py (for merging across single-sample VCF)<br /> ***These two programs are available at /net/wonderland/home/yancylo/bin/umake-glfSingle<br /> **To generate the Makefile corresponding to this new pipeline flow, do:<br /> perl /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl --conf /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf<br /> <br /> ==Customization==<br /> *To change paths to glfSingle and merge_glfS_vcf.py, go to the following lines of umake-glfSingle.pl:<br /> **line 1000 - my $cmd = "python [your-path]/merge_glfS_vcf.py --file-list $glfAlias --chr $chr --outfile $vcf > $vcf.log";<br /> **line 1073 - $cmd .= "\n\t".&getMosixCmd("[your-path]/glfSingle -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference > $smVcf.log");<br /> *To apply the uniform Ts/Tv model to glfSingle, go to the following line of umake-glfSingle.pl and make the changes in bold:<br /> **line 1073 - $cmd .= "\n\t".&getMosixCmd("/net/wonderland/home/yancylo/bin/umake-glfSingle/'''glfSingle_ut''' -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference '''--uniformTsTv''' > $smVcf.log");<br /> <br /> ==Remarks==<br /> *The --reference option should be enabled for glfSingle, such that it calls the homozygous reference genotypes per sample. This is necessary to distinguish between homref and missing genotypes during merging.<br /> *The merging program combines across individual-sample VCFs in small chunks of positions, hence it does NOT create a memory issue even when merging across large sample sizes and big regions.<br /> *One potential concern of this pipeline is the number and size of additional files, since each sample now has its own set of VCFs (~2Gb for chr20 per sample).<br /> <br /> ==Contact==<br /> Please contact Yancy if you have any questions.</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=UMAKE-glfSingle&diff=9365 UMAKE-glfSingle 2014-01-15T21:51:13Z

<p>Yancylo: /* Ingredients */</p> <hr /> <div>This is a modification of UMAKE to incorporate an individual-based variant caller in the pipeline.<br /> <br /> The idea is to use glfSingle to generate sample-specific VCF after pileup, and then replace the glfMultiples step by a merging step. The merging generates a population VCF that looks the same as what would have been the glfMultiples output. Subsequent filtering and imputation steps can follow as usual.<br /> <br /> ==Ingredients==<br /> *Index file<br /> **same as original UMAKE index<br /> **An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.index<br /> *Configuration file<br /> **same as original UMAKE conf<br /> **An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf<br /> **Note that the glfSingle and merging steps are included by enabling these two steps:<br /> RUN_PILEUP = TRUE # create GLF file from BAM then individual VCF using glfSingle<br /> RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls, population VCF by merging the glfSingle outputs<br /> <br /> *Perl script for generating Makefile<br /> **Found at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl<br /> **It is modified from umake.pl to call glfSingle and merge_glfS_vcf.py (for merging across single-sample VCF)<br /> ***These two programs are available at /net/wonderland/home/yancylo/bin/umake-glfSingle<br /> **To generate the Makefile corresponding to this new pipeline flow, do:<br /> perl /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl --conf /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf<br /> <br /> ==Customization==<br /> *To change paths to glfSingle and merge_glfS_vcf.py, go to the following lines of umake-glfSingle.pl:<br /> **line 1000 - my $cmd = "python [your-path]/merge_glfS_vcf.py --file-list $glfAlias --chr $chr --outfile $vcf > $vcf.log";<br /> **line 1073 - $cmd .= "\n\t".&getMosixCmd("[your-path]/glfSingle -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference > $smVcf.log");<br /> *To apply the uniform Ts/Tv model to glfSingle, go to the following line of umake-glfSingle.pl and make the changes in bold:<br /> **line 1073 - $cmd .= "\n\t".&getMosixCmd("/net/wonderland/home/yancylo/bin/umake-glfSingle/'''glfSingle_ut''' -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference '''--uniformTsTv''' > $smVcf.log");<br /> <br /> ==Remarks==<br /> *The --reference option should be enabled for glfSingle, such that it calls the homozygous reference genotypes per sample. This is necessary to distinguish between homref and missing genotypes during merging.<br /> *The merging program combines across individual-sample VCFs in small chunks of positions, hence it does NOT create a memory issue even when merging across large sample sizes and big regions.<br /> *One potential concern of this pipeline is the number and size of additional files, since each sample now has its own set of VCFs (~2Gb for chr20 per sample).<br /> <br /> ==Contact==<br /> Please contact Yancy if you have any questions.</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=UMAKE-glfSingle&diff=9364 UMAKE-glfSingle 2014-01-15T20:08:03Z

<p>Yancylo: /* Remarks */</p> <hr /> <div>This is a modification of UMAKE to incorporate an individual-based variant caller in the pipeline.<br /> <br /> The idea is to use glfSingle to generate sample-specific VCF after pileup, and then replace the glfMultiples step by a merging step. The merging generates a population VCF that looks the same as what would have been the glfMultiples output. Subsequent filtering and imputation steps can follow as usual.<br /> <br /> ==Ingredients==<br /> *Index file - same as original UMAKE index. An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.index<br /> *Configuration file - same as original UMAKE conf. An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf . Note that the glfSingle and merging steps are included by enabling these two steps:<br /> RUN_PILEUP = TRUE # create GLF file from BAM then individual VCF using glfSingle<br /> RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls, population VCF by merging the glfSingle outputs<br /> <br /> *Perl script for generating Makefile - /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl . It is modified from umake.pl to call glfSingle and merge_glfS_vcf.py (for merging across single-sample VCF).<br /> **These two programs are available at /net/wonderland/home/yancylo/bin/umake-glfSingle<br /> **To generate the Makefile corresponding to this new pipeline flow, do:<br /> perl /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl --conf /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf<br /> <br /> ==Customization==<br /> *To change paths to glfSingle and merge_glfS_vcf.py, go to the following lines of umake-glfSingle.pl:<br /> **line 1000 - my $cmd = "python [your-path]/merge_glfS_vcf.py --file-list $glfAlias --chr $chr --outfile $vcf > $vcf.log";<br /> **line 1073 - $cmd .= "\n\t".&getMosixCmd("[your-path]/glfSingle -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference > $smVcf.log");<br /> *To apply the uniform Ts/Tv model to glfSingle, go to the following line of umake-glfSingle.pl and make the changes in bold:<br /> **line 1073 - $cmd .= "\n\t".&getMosixCmd("/net/wonderland/home/yancylo/bin/umake-glfSingle/'''glfSingle_ut''' -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference '''--uniformTsTv''' > $smVcf.log");<br /> <br /> ==Remarks==<br /> *The --reference option should be enabled for glfSingle, such that it calls the homozygous reference genotypes per sample. This is necessary to distinguish between homref and missing genotypes during merging.<br /> *The merging program combines across individual-sample VCFs in small chunks of positions, hence it does NOT create a memory issue even when merging across large sample sizes and big regions.<br /> *One potential concern of this pipeline is the number and size of additional files, since each sample now has its own set of VCFs (~2Gb for chr20 per sample).<br /> <br /> ==Contact==<br /> Please contact Yancy if you have any questions.</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=UMAKE-glfSingle&diff=9363 UMAKE-glfSingle 2014-01-15T20:07:28Z

<p>Yancylo: </p> <hr /> <div>This is a modification of UMAKE to incorporate an individual-based variant caller in the pipeline.<br /> <br /> The idea is to use glfSingle to generate sample-specific VCF after pileup, and then replace the glfMultiples step by a merging step. The merging generates a population VCF that looks the same as what would have been the glfMultiples output. Subsequent filtering and imputation steps can follow as usual.<br /> <br /> ==Ingredients==<br /> *Index file - same as original UMAKE index. An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.index<br /> *Configuration file - same as original UMAKE conf. An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf . Note that the glfSingle and merging steps are included by enabling these two steps:<br /> RUN_PILEUP = TRUE # create GLF file from BAM then individual VCF using glfSingle<br /> RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls, population VCF by merging the glfSingle outputs<br /> <br /> *Perl script for generating Makefile - /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl . It is modified from umake.pl to call glfSingle and merge_glfS_vcf.py (for merging across single-sample VCF).<br /> **These two programs are available at /net/wonderland/home/yancylo/bin/umake-glfSingle<br /> **To generate the Makefile corresponding to this new pipeline flow, do:<br /> perl /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl --conf /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf<br /> <br /> ==Customization==<br /> *To change paths to glfSingle and merge_glfS_vcf.py, go to the following lines of umake-glfSingle.pl:<br /> **line 1000 - my $cmd = "python [your-path]/merge_glfS_vcf.py --file-list $glfAlias --chr $chr --outfile $vcf > $vcf.log";<br /> **line 1073 - $cmd .= "\n\t".&getMosixCmd("[your-path]/glfSingle -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference > $smVcf.log");<br /> *To apply the uniform Ts/Tv model to glfSingle, go to the following line of umake-glfSingle.pl and make the changes in bold:<br /> **line 1073 - $cmd .= "\n\t".&getMosixCmd("/net/wonderland/home/yancylo/bin/umake-glfSingle/'''glfSingle_ut''' -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference '''--uniformTsTv''' > $smVcf.log");<br /> <br /> ==Remarks==<br /> *The --reference option should be enabled for glfSingle, such that it calls the homozygous reference genotypes per sample. This is necessary to distinguish between homref and missing genotypes during merging.<br /> *The merging program combines across individual-sample VCFs in small chunks of positions, hence it does NOT create a memory issue even when merging across large sample sizes and big regions.<br /> *One potential concern of this pipeline is file size, since each sample now has its own VCFs (~2Gb for chr20 per sample).<br /> <br /> ==Contact==<br /> Please contact Yancy if you have any questions.</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=UMAKE-glfSingle&diff=9362 UMAKE-glfSingle 2014-01-15T19:54:15Z

<p>Yancylo: </p> <hr /> <div>This is a modification of UMAKE to incorporate an individual-based variant caller in the pipeline.<br /> <br /> The idea is to use glfSingle to generate sample-specific VCF after pileup, and then replace the glfMultiples step by a merging step. The merging generates a population VCF that looks the same as what would have been the glfMultiples output. Subsequent filtering and imputation steps can follow as usual.<br /> <br /> Ingredients:<br /> *Index file - same as original UMAKE index. An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.index<br /> *Configuration file - same as original UMAKE conf. An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf . Note that the glfSingle and merging steps are included by enabling these two steps:<br /> RUN_PILEUP = TRUE # create GLF file from BAM then individual VCF using glfSingle<br /> RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls, population VCF by merging the glfSingle outputs<br /> <br /> *Perl script for generating Makefile - /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl . It is modified from umake.pl to call glfSingle and merge_glfS_vcf.py (for merging across single-sample VCF).<br /> **These two programs are available at /net/wonderland/home/yancylo/bin/umake-glfSingle<br /> **To generate the Makefile corresponding to this new pipeline flow, do:<br /> perl /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl --conf /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf<br /> <br /> Customization:<br /> *To change paths to glfSingle and merge_glfS_vcf.py, go to the following lines of umake-glfSingle.pl:<br /> **line 1000 - my $cmd = "python [your-path]/merge_glfS_vcf.py --file-list $glfAlias --chr $chr --outfile $vcf > $vcf.log";<br /> **line 1073 - $cmd .= "\n\t".&getMosixCmd("[your-path]/glfSingle -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference > $smVcf.log");<br /> *To apply the uniform Ts/Tv model to glfSingle, go to the following line of umake-glfSingle.pl and make the changes in bold:<br /> **line 1073 - $cmd .= "\n\t".&getMosixCmd("/net/wonderland/home/yancylo/bin/umake-glfSingle/'''glfSingle_ut''' -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference '''--uniformTsTv''' > $smVcf.log");</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=UMAKE-glfSingle&diff=9361 UMAKE-glfSingle 2014-01-15T19:49:39Z

<p>Yancylo: </p> <hr /> <div>This is a modification of UMAKE to incorporate an individual-based variant caller in the pipeline.<br /> <br /> The idea is to use glfSingle to generate sample-specific VCF after pileup, and then replace the glfMultiples step by a merging step. The merging generates a population VCF that looks the same as what would have been the glfMultiples output. Subsequent filtering and imputation steps can follow as usual.<br /> <br /> Ingredients:<br /> *Index file - same as original UMAKE index. An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.index<br /> *Configuration file - same as original UMAKE conf. An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf . Note that the glfSingle and merging steps are implicitly included in these two steps:<br /> RUN_PILEUP = TRUE # create GLF file from BAM then individual VCF using glfSingle<br /> RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls, population VCF by merging the glfSingle outputs<br /> <br /> *Perl script for generating Makefile - /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl . It is modified from umake.pl:<br /> **calls glfSingle and merge_glfS_vcf.py (for merging across single-sample VCF) from /net/wonderland/home/yancylo/bin/umake-glfSingle<br /> **To generate the Makefile corresponding to this new pipeline flow, do:<br /> perl /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl --conf /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf<br /> <br /> Customization:<br /> *To change paths to glfSingle and merge_glfS_vcf.py, go to the following lines of umake-glfSingle.pl:<br /> **line 1000 - my $cmd = "python [your-path]/merge_glfS_vcf.py --file-list $glfAlias --chr $chr --outfile $vcf > $vcf.log";<br /> **line 1073 - $cmd .= "\n\t".&getMosixCmd("[your-path]/glfSingle -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference > $smVcf.log");<br /> *To apply the uniform Ts/Tv model to glfSingle, go to the following line of umake-glfSingle.pl and make the changes in bold:<br /> **line 1073 - $cmd .= "\n\t".&getMosixCmd("/net/wonderland/home/yancylo/bin/umake-glfSingle/'''glfSingle_ut''' -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference '''--uniformTsTv''' > $smVcf.log");</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=UMAKE-glfSingle&diff=9360 UMAKE-glfSingle 2014-01-15T19:46:44Z

<p>Yancylo: Created page with "This is a modification of UMAKE to incorporate an individual-based variant caller in the pipeline. The idea is to use glfSingle to generate sample-specific VCF after pileup, ..."</p> <hr /> <div>This is a modification of UMAKE to incorporate an individual-based variant caller in the pipeline.<br /> <br /> The idea is to use glfSingle to generate sample-specific VCF after pileup, and then replace the glfMultiples step by a merging step. The merging generates a population VCF that looks the same as what would have been the glfMultiples output. Subsequent filtering and imputation steps can follow as usual.<br /> <br /> Ingredients:<br /> *Index file - same as original UMAKE index. An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.index<br /> *Configuration file - same as original UMAKE conf. An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf . Note that the glfSingle and merging steps are implicitly included in these two steps:<br /> RUN_PILEUP = TRUE # create GLF file from BAM then individual VCF using glfSingle<br /> RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls, population VCF by merging the glfSingle outputs<br /> <br /> *Perl script for generating Makefile - /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl . It is modified from umake.pl:<br /> **calls glfSingle and merge_glfS_vcf.py (for merging across single-sample VCF) from /net/wonderland/home/yancylo/bin/umake-glfSingle<br /> **To generate the Makefile corresponding to this new pipeline flow, do:<br /> perl /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl --conf /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf<br /> **To change paths to glfSingle and merge_glfS_vcf.py, go to the following lines of umake-glfSingle.pl:<br /> ***line 1000 - my $cmd = "python [your-path]/merge_glfS_vcf.py --file-list $glfAlias --chr $chr --outfile $vcf > $vcf.log";<br /> ***line 1073 - $cmd .= "\n\t".&getMosixCmd("[your-path]/glfSingle -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference --uniformTsTv > $smVcf.log");</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=GlfSingle&diff=8745 GlfSingle 2013-09-26T15:34:41Z

<p>Yancylo: /* Model for Variant Calling */</p> <hr /> <div>[[Category:Software]]<br /> '''glfSingle''' is a [[GLF]]-based variant caller for next-generation sequencing data. It takes a [[GLF]] format genotype likelihood file as input and generates a [[VCF]]-format set of variant calls as output.<br /> <br /> == Basic Usage Example ==<br /> <br /> Here is an example of how <code>glfSingle</code> works:<br /> <br /> glfSingle -g NA19240.chrom20.SLX.glf -b NA19240.chrom20.SLX.vcf > NA19240.chrom20.SLX.log<br /> <br /> == Command Line Options ==<br /> <br /> -g ''genotype likelihood file'' Specifies the name of the input [[GLF]]-format genotype likelihood file<br /> -b ''base call file'' Specifies the name of the output [[VCF]]-format base call file<br /> -s ''sample label'' Specifies a label for the sample being analyzed, which will be included in the output VCF file<br /> -p ''threshold'' The threshold for base calling. Base calls will be made when their posterior likelihood exceeds ''threshold''<br /> <br /> --minMapQuality ''threshold'' Positions where the root-means squared mapping quality falls below this threshold will be excluded.<br /> --minDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded.<br /> --maxDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded.<br /> --reference Positions called as homozygous reference will be included in the output.<br /> <br /> To learn about default values for these options, simply run the program with no arguments.<br /> <br /> == Model for Variant Calling ==<br /> glfSingle uses a likelihood-based model for variant calling. Starting from genotype likelihoods ''Pr(reads| genotype)'' per genomic position, computed from appropriate tools (eg. Samtools BAQ), the likelihoods combine with an individual-based prior ''p(genotype)'' to generate posterior probabilities ''Pr(genotype| reads)''. <br /> <br /> Ingredients that go into prior:<br /> *All sites have an equal probability of showing polymorphism:<br /> **P(non-reference base) = 0.001<br /> *When a site shows polymorphism, it is usually heterozygous:<br /> **P(non-reference heterozygote) = 0.01 * 2/3<br /> **P(non-reference homozygote) = 0.01 * 1/3<br /> *Mutation model: Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account for minority of variants<br /> **transition has 2/3 probability<br /> **each transversion has 1/6 probability<br /> <br /> *'''New implementation''': Alternative mutation model with uniform (uninformative) prior for transition to transversion ratio<br /> **updated by Yancy Lo, 9/24/2012<br /> **each mutation has a 1/3 probability<br /> **add --uniformTsTv in command line to enable this alternative mutation model<br /> **download glfSingle with this new implementation here: [[File:Generic-glfSingle-2013-09-25.tar.gz]]<br /> <br /> == Download ==<br /> <br /> For the current of glfSingle, please go to [http://www.sph.umich.edu/csg/abecasis/glfTools/ our GLF Tools Website].<br /> <br /> == TODO ==<br /> <br /> Support for X chromosome variant calling.<br /> <br /> Support for a two pass depth filter that uses the data to automatically work out appropriate filtering thresholds.</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=GlfSingle&diff=8744 GlfSingle 2013-09-26T15:34:16Z

<p>Yancylo: /* Model for Variant Calling */</p> <hr /> <div>[[Category:Software]]<br /> '''glfSingle''' is a [[GLF]]-based variant caller for next-generation sequencing data. It takes a [[GLF]] format genotype likelihood file as input and generates a [[VCF]]-format set of variant calls as output.<br /> <br /> == Basic Usage Example ==<br /> <br /> Here is an example of how <code>glfSingle</code> works:<br /> <br /> glfSingle -g NA19240.chrom20.SLX.glf -b NA19240.chrom20.SLX.vcf > NA19240.chrom20.SLX.log<br /> <br /> == Command Line Options ==<br /> <br /> -g ''genotype likelihood file'' Specifies the name of the input [[GLF]]-format genotype likelihood file<br /> -b ''base call file'' Specifies the name of the output [[VCF]]-format base call file<br /> -s ''sample label'' Specifies a label for the sample being analyzed, which will be included in the output VCF file<br /> -p ''threshold'' The threshold for base calling. Base calls will be made when their posterior likelihood exceeds ''threshold''<br /> <br /> --minMapQuality ''threshold'' Positions where the root-means squared mapping quality falls below this threshold will be excluded.<br /> --minDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded.<br /> --maxDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded.<br /> --reference Positions called as homozygous reference will be included in the output.<br /> <br /> To learn about default values for these options, simply run the program with no arguments.<br /> <br /> == Model for Variant Calling ==<br /> glfSingle uses a likelihood-based model for variant calling. Starting from genotype likelihoods ''Pr(reads| genotype)'' per genomic position, computed from appropriate tools (eg. Samtools BAQ), the likelihoods combine with an individual-based prior ''p(genotype)'' to generate posterior probabilities ''Pr(genotype| reads)''. <br /> <br /> Ingredients that go into prior:<br /> *All sites have an equal probability of showing polymorphism:<br /> **P(non-reference base) = 0.001<br /> *When a site shows polymorphism, it is usually heterozygous:<br /> **P(non-reference heterozygote) = 0.01 * 2/3<br /> **P(non-reference homozygote) = 0.01 * 1/3<br /> *Mutation model: Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account for minority of variants<br /> **transition has 2/3 probability<br /> **each transversion has 1/6 probability<br /> <br /> *'''New implementation''': Alternative mutation model with uniform (uninformative) prior for transition to transversion ratio<br /> **updated by Yancy Lo, 9/24/2012<br /> **each mutation has a 1/3 probability<br /> **add --uniformTsTv in command line to enable this alternative mutation model<br /> **download [[File:Generic-glfSingle-2013-09-25.tar.gz]]<br /> <br /> == Download ==<br /> <br /> For the current of glfSingle, please go to [http://www.sph.umich.edu/csg/abecasis/glfTools/ our GLF Tools Website].<br /> <br /> == TODO ==<br /> <br /> Support for X chromosome variant calling.<br /> <br /> Support for a two pass depth filter that uses the data to automatically work out appropriate filtering thresholds.</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=File:Generic-glfSingle-2013-09-25.tar.gz&diff=8743 File:Generic-glfSingle-2013-09-25.tar.gz 2013-09-26T15:31:59Z

<p>Yancylo: glfSingle with uniform Ts/Tv option</p> <hr /> <div>glfSingle with uniform Ts/Tv option</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=GlfSingle&diff=8742 GlfSingle 2013-09-25T20:16:11Z

<p>Yancylo: /* Model for Variant Calling */</p> <hr /> <div>[[Category:Software]]<br /> '''glfSingle''' is a [[GLF]]-based variant caller for next-generation sequencing data. It takes a [[GLF]] format genotype likelihood file as input and generates a [[VCF]]-format set of variant calls as output.<br /> <br /> == Basic Usage Example ==<br /> <br /> Here is an example of how <code>glfSingle</code> works:<br /> <br /> glfSingle -g NA19240.chrom20.SLX.glf -b NA19240.chrom20.SLX.vcf > NA19240.chrom20.SLX.log<br /> <br /> == Command Line Options ==<br /> <br /> -g ''genotype likelihood file'' Specifies the name of the input [[GLF]]-format genotype likelihood file<br /> -b ''base call file'' Specifies the name of the output [[VCF]]-format base call file<br /> -s ''sample label'' Specifies a label for the sample being analyzed, which will be included in the output VCF file<br /> -p ''threshold'' The threshold for base calling. Base calls will be made when their posterior likelihood exceeds ''threshold''<br /> <br /> --minMapQuality ''threshold'' Positions where the root-means squared mapping quality falls below this threshold will be excluded.<br /> --minDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded.<br /> --maxDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded.<br /> --reference Positions called as homozygous reference will be included in the output.<br /> <br /> To learn about default values for these options, simply run the program with no arguments.<br /> <br /> == Model for Variant Calling ==<br /> glfSingle uses a likelihood-based model for variant calling. Starting from genotype likelihoods ''Pr(reads| genotype)'' per genomic position, computed from appropriate tools (eg. Samtools BAQ), the likelihoods combine with an individual-based prior ''p(genotype)'' to generate posterior probabilities ''Pr(genotype| reads)''. <br /> <br /> Ingredients that go into prior:<br /> *All sites have an equal probability of showing polymorphism:<br /> **P(non-reference base) = 0.001<br /> *When a site shows polymorphism, it is usually heterozygous:<br /> **P(non-reference heterozygote) = 0.01 * 2/3<br /> **P(non-reference homozygote) = 0.01 * 1/3<br /> *Mutation model: Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account for minority of variants<br /> **transition has 2/3 probability<br /> **each transversion has 1/6 probability<br /> <br /> *'''New implementation''': Alternative mutation model with uniform (uninformative) prior for transition to transversion ratio<br /> **updated by Yancy Lo, 9/24/2012<br /> **each mutation has a 1/3 probability<br /> **add --uniformTsTv in command line to enable this alternative mutation model<br /> **download [[here ]]<br /> <br /> == Download ==<br /> <br /> For the current of glfSingle, please go to [http://www.sph.umich.edu/csg/abecasis/glfTools/ our GLF Tools Website].<br /> <br /> == TODO ==<br /> <br /> Support for X chromosome variant calling.<br /> <br /> Support for a two pass depth filter that uses the data to automatically work out appropriate filtering thresholds.</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=GlfSingle&diff=8741 GlfSingle 2013-09-25T20:15:39Z

<p>Yancylo: /* Model for Variant Calling */</p> <hr /> <div>[[Category:Software]]<br /> '''glfSingle''' is a [[GLF]]-based variant caller for next-generation sequencing data. It takes a [[GLF]] format genotype likelihood file as input and generates a [[VCF]]-format set of variant calls as output.<br /> <br /> == Basic Usage Example ==<br /> <br /> Here is an example of how <code>glfSingle</code> works:<br /> <br /> glfSingle -g NA19240.chrom20.SLX.glf -b NA19240.chrom20.SLX.vcf > NA19240.chrom20.SLX.log<br /> <br /> == Command Line Options ==<br /> <br /> -g ''genotype likelihood file'' Specifies the name of the input [[GLF]]-format genotype likelihood file<br /> -b ''base call file'' Specifies the name of the output [[VCF]]-format base call file<br /> -s ''sample label'' Specifies a label for the sample being analyzed, which will be included in the output VCF file<br /> -p ''threshold'' The threshold for base calling. Base calls will be made when their posterior likelihood exceeds ''threshold''<br /> <br /> --minMapQuality ''threshold'' Positions where the root-means squared mapping quality falls below this threshold will be excluded.<br /> --minDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded.<br /> --maxDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded.<br /> --reference Positions called as homozygous reference will be included in the output.<br /> <br /> To learn about default values for these options, simply run the program with no arguments.<br /> <br /> == Model for Variant Calling ==<br /> glfSingle uses a likelihood-based model for variant calling. Starting from genotype likelihoods ''Pr(reads| genotype)'' per genomic position, computed from appropriate tools (eg. Samtools BAQ), the likelihoods combine with an individual-based prior ''p(genotype)'' to generate posterior probabilities ''Pr(genotype| reads)''. <br /> <br /> Ingredients that go into prior:<br /> *All sites have an equal probability of showing polymorphism:<br /> **P(non-reference base) = 0.001<br /> *When a site shows polymorphism, it is usually heterozygous:<br /> **P(non-reference heterozygote) = 0.01 * 2/3<br /> **P(non-reference homozygote) = 0.01 * 1/3<br /> *Mutation model: Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account for minority of variants<br /> **transition has 2/3 probability<br /> **each transversion has 1/6 probability<br /> <br /> *'''New implementation''': Alternative mutation model with uniform (uninformative) prior for transition to transversion ratio<br /> **each mutation has a 1/3 probability<br /> **add --uniformTsTv in command line to enable this alternative mutation model<br /> **download [here ]<br /> <br /> == Download ==<br /> <br /> For the current of glfSingle, please go to [http://www.sph.umich.edu/csg/abecasis/glfTools/ our GLF Tools Website].<br /> <br /> == TODO ==<br /> <br /> Support for X chromosome variant calling.<br /> <br /> Support for a two pass depth filter that uses the data to automatically work out appropriate filtering thresholds.</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=GlfSingle&diff=8740 GlfSingle 2013-09-25T20:14:26Z

<p>Yancylo: /* Command Line Options */</p> <hr /> <div>[[Category:Software]]<br /> '''glfSingle''' is a [[GLF]]-based variant caller for next-generation sequencing data. It takes a [[GLF]] format genotype likelihood file as input and generates a [[VCF]]-format set of variant calls as output.<br /> <br /> == Basic Usage Example ==<br /> <br /> Here is an example of how <code>glfSingle</code> works:<br /> <br /> glfSingle -g NA19240.chrom20.SLX.glf -b NA19240.chrom20.SLX.vcf > NA19240.chrom20.SLX.log<br /> <br /> == Command Line Options ==<br /> <br /> -g ''genotype likelihood file'' Specifies the name of the input [[GLF]]-format genotype likelihood file<br /> -b ''base call file'' Specifies the name of the output [[VCF]]-format base call file<br /> -s ''sample label'' Specifies a label for the sample being analyzed, which will be included in the output VCF file<br /> -p ''threshold'' The threshold for base calling. Base calls will be made when their posterior likelihood exceeds ''threshold''<br /> <br /> --minMapQuality ''threshold'' Positions where the root-means squared mapping quality falls below this threshold will be excluded.<br /> --minDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded.<br /> --maxDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded.<br /> --reference Positions called as homozygous reference will be included in the output.<br /> <br /> To learn about default values for these options, simply run the program with no arguments.<br /> <br /> == Model for Variant Calling ==<br /> glfSingle uses a likelihood-based model for variant calling. Starting from genotype likelihoods ''Pr(reads| genotype)'' per genomic position, computed from appropriate tools (eg. Samtools BAQ), the likelihoods combine with an individual-based prior ''p(genotype)'' to generate posterior probabilities ''Pr(genotype| reads)''. <br /> <br /> Ingredients that go into prior:<br /> *All sites have an equal probability of showing polymorphism:<br /> **P(non-reference base) = 0.001<br /> *When a site shows polymorphism, it is usually heterozygous:<br /> **P(non-reference heterozygote) = 0.01 * 2/3<br /> **P(non-reference homozygote) = 0.01 * 1/3<br /> *Mutation model: Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account for minority of variants<br /> **transition has 2/3 probability<br /> **each transversion has 1/6 probability<br /> <br /> *New implementation: Alternative mutation model with uniform (uninformative) prior for transition to transversion ratio<br /> **each mutation has a 1/3 probability<br /> **add --uniformTsTv in command line to enable this alternative mutation model<br /> **download here<br /> <br /> == Download ==<br /> <br /> For the current of glfSingle, please go to [http://www.sph.umich.edu/csg/abecasis/glfTools/ our GLF Tools Website].<br /> <br /> == TODO ==<br /> <br /> Support for X chromosome variant calling.<br /> <br /> Support for a two pass depth filter that uses the data to automatically work out appropriate filtering thresholds.</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=GlfSingle&diff=8739 GlfSingle 2013-09-25T20:14:09Z

<p>Yancylo: /* Model for Variant Calling */</p> <hr /> <div>[[Category:Software]]<br /> '''glfSingle''' is a [[GLF]]-based variant caller for next-generation sequencing data. It takes a [[GLF]] format genotype likelihood file as input and generates a [[VCF]]-format set of variant calls as output.<br /> <br /> == Basic Usage Example ==<br /> <br /> Here is an example of how <code>glfSingle</code> works:<br /> <br /> glfSingle -g NA19240.chrom20.SLX.glf -b NA19240.chrom20.SLX.vcf > NA19240.chrom20.SLX.log<br /> <br /> == Command Line Options ==<br /> <br /> -g ''genotype likelihood file'' Specifies the name of the input [[GLF]]-format genotype likelihood file<br /> -b ''base call file'' Specifies the name of the output [[VCF]]-format base call file<br /> -s ''sample label'' Specifies a label for the sample being analyzed, which will be included in the output VCF file<br /> -p ''threshold'' The threshold for base calling. Base calls will be made when their posterior likelihood exceeds ''threshold''<br /> <br /> --minMapQuality ''threshold'' Positions where the root-means squared mapping quality falls below this threshold will be excluded.<br /> --minDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded.<br /> --maxDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded.<br /> --reference Positions called as homozygous reference will be included in the output.<br /> --uniformTsTv Use a uniform prior for transition-to-transversion ratio. <br /> <br /> To learn about default values for these options, simply run the program with no arguments.<br /> <br /> == Model for Variant Calling ==<br /> glfSingle uses a likelihood-based model for variant calling. Starting from genotype likelihoods ''Pr(reads| genotype)'' per genomic position, computed from appropriate tools (eg. Samtools BAQ), the likelihoods combine with an individual-based prior ''p(genotype)'' to generate posterior probabilities ''Pr(genotype| reads)''. <br /> <br /> Ingredients that go into prior:<br /> *All sites have an equal probability of showing polymorphism:<br /> **P(non-reference base) = 0.001<br /> *When a site shows polymorphism, it is usually heterozygous:<br /> **P(non-reference heterozygote) = 0.01 * 2/3<br /> **P(non-reference homozygote) = 0.01 * 1/3<br /> *Mutation model: Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account for minority of variants<br /> **transition has 2/3 probability<br /> **each transversion has 1/6 probability<br /> <br /> *New implementation: Alternative mutation model with uniform (uninformative) prior for transition to transversion ratio<br /> **each mutation has a 1/3 probability<br /> **add --uniformTsTv in command line to enable this alternative mutation model<br /> **download here<br /> <br /> == Download ==<br /> <br /> For the current of glfSingle, please go to [http://www.sph.umich.edu/csg/abecasis/glfTools/ our GLF Tools Website].<br /> <br /> == TODO ==<br /> <br /> Support for X chromosome variant calling.<br /> <br /> Support for a two pass depth filter that uses the data to automatically work out appropriate filtering thresholds.</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=GlfSingle&diff=8706 GlfSingle 2013-09-23T19:32:14Z

<p>Yancylo: /* Model for Variant Calling */</p> <hr /> <div>[[Category:Software]]<br /> '''glfSingle''' is a [[GLF]]-based variant caller for next-generation sequencing data. It takes a [[GLF]] format genotype likelihood file as input and generates a [[VCF]]-format set of variant calls as output.<br /> <br /> == Basic Usage Example ==<br /> <br /> Here is an example of how <code>glfSingle</code> works:<br /> <br /> glfSingle -g NA19240.chrom20.SLX.glf -b NA19240.chrom20.SLX.vcf > NA19240.chrom20.SLX.log<br /> <br /> == Command Line Options ==<br /> <br /> -g ''genotype likelihood file'' Specifies the name of the input [[GLF]]-format genotype likelihood file<br /> -b ''base call file'' Specifies the name of the output [[VCF]]-format base call file<br /> -s ''sample label'' Specifies a label for the sample being analyzed, which will be included in the output VCF file<br /> -p ''threshold'' The threshold for base calling. Base calls will be made when their posterior likelihood exceeds ''threshold''<br /> <br /> --minMapQuality ''threshold'' Positions where the root-means squared mapping quality falls below this threshold will be excluded.<br /> --minDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded.<br /> --maxDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded.<br /> --reference Positions called as homozygous reference will be included in the output.<br /> --uniformTsTv Use a uniform prior for transition-to-transversion ratio. <br /> <br /> To learn about default values for these options, simply run the program with no arguments.<br /> <br /> == Model for Variant Calling ==<br /> glfSingle uses a likelihood-based model for variant calling. Starting from genotype likelihoods ''Pr(reads| genotype)'' per genomic position, computed from appropriate tools (eg. Samtools BAQ), the likelihoods combine with an individual-based prior ''p(genotype)'' to generate posterior probabilities ''Pr(genotype| reads)''. <br /> <br /> Ingredients that go into prior:<br /> *All sites have an equal probability of showing polymorphism:<br /> **P(non-reference base) = 0.001<br /> *When a site shows polymorphism, it is usually heterozygous:<br /> **P(non-reference heterozygote) = 0.01 * 2/3<br /> **P(non-reference homozygote) = 0.01 * 1/3<br /> *Two options of mutation model:<br /> **Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account for minority of variants<br /> ***transition has 2/3 probability<br /> ***each transversion has 1/6 probability<br /> **Uniform (uninformative) prior for transition to transversion ratio<br /> ***each mutation has a 1/3 probability<br /> <br /> == Download ==<br /> <br /> For the current of glfSingle, please go to [http://www.sph.umich.edu/csg/abecasis/glfTools/ our GLF Tools Website].<br /> <br /> == TODO ==<br /> <br /> Support for X chromosome variant calling.<br /> <br /> Support for a two pass depth filter that uses the data to automatically work out appropriate filtering thresholds.</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=GlfSingle&diff=8705 GlfSingle 2013-09-23T19:23:51Z

<p>Yancylo: /* Command Line Options */</p> <hr /> <div>[[Category:Software]]<br /> '''glfSingle''' is a [[GLF]]-based variant caller for next-generation sequencing data. It takes a [[GLF]] format genotype likelihood file as input and generates a [[VCF]]-format set of variant calls as output.<br /> <br /> == Basic Usage Example ==<br /> <br /> Here is an example of how <code>glfSingle</code> works:<br /> <br /> glfSingle -g NA19240.chrom20.SLX.glf -b NA19240.chrom20.SLX.vcf > NA19240.chrom20.SLX.log<br /> <br /> == Command Line Options ==<br /> <br /> -g ''genotype likelihood file'' Specifies the name of the input [[GLF]]-format genotype likelihood file<br /> -b ''base call file'' Specifies the name of the output [[VCF]]-format base call file<br /> -s ''sample label'' Specifies a label for the sample being analyzed, which will be included in the output VCF file<br /> -p ''threshold'' The threshold for base calling. Base calls will be made when their posterior likelihood exceeds ''threshold''<br /> <br /> --minMapQuality ''threshold'' Positions where the root-means squared mapping quality falls below this threshold will be excluded.<br /> --minDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded.<br /> --maxDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded.<br /> --reference Positions called as homozygous reference will be included in the output.<br /> --uniformTsTv Use a uniform prior for transition-to-transversion ratio. <br /> <br /> To learn about default values for these options, simply run the program with no arguments.<br /> <br /> == Model for Variant Calling ==<br /> glfSingle uses a likelihood-based model for variant calling. Starting from genotype likelihoods ''Pr(reads| genotype)'' per genomic position, computed from appropriate tools (eg. Samtools BAQ), the likelihoods combine with an individual-based prior ''p(genotype)'' to generate posterior probabilities ''Pr(genotype| reads)''. <br /> <br /> Ingredients that go into prior:<br /> *All sites have an equal probability of showing polymorphism:<br /> **P(non-reference base) = 0.001<br /> *When a site shows polymorphism, it is usually heterozygous:<br /> **P(non-reference heterozygote) = 0.01 * 2/3<br /> **P(non-reference homozygote) = 0.01 * 1/3<br /> *Two options of mutation model:<br /> **Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account for minority of variants<br /> **Uniform prior for transition to transversion ratio (1:1)<br /> <br /> == Download ==<br /> <br /> For the current of glfSingle, please go to [http://www.sph.umich.edu/csg/abecasis/glfTools/ our GLF Tools Website].<br /> <br /> == TODO ==<br /> <br /> Support for X chromosome variant calling.<br /> <br /> Support for a two pass depth filter that uses the data to automatically work out appropriate filtering thresholds.</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=GlfSingle&diff=8704 GlfSingle 2013-09-23T19:19:23Z

<p>Yancylo: /* Command Line Options */</p> <hr /> <div>[[Category:Software]]<br /> '''glfSingle''' is a [[GLF]]-based variant caller for next-generation sequencing data. It takes a [[GLF]] format genotype likelihood file as input and generates a [[VCF]]-format set of variant calls as output.<br /> <br /> == Basic Usage Example ==<br /> <br /> Here is an example of how <code>glfSingle</code> works:<br /> <br /> glfSingle -g NA19240.chrom20.SLX.glf -b NA19240.chrom20.SLX.vcf > NA19240.chrom20.SLX.log<br /> <br /> == Command Line Options ==<br /> <br /> -g ''genotype likelihood file'' Specifies the name of the input [[GLF]]-format genotype likelihood file<br /> -b ''base call file'' Specifies the name of the output [[VCF]]-format base call file<br /> -s ''sample label'' Specifies a label for the sample being analyzed, which will be included in the output VCF file<br /> -p ''threshold'' The threshold for base calling. Base calls will be made when their posterior likelihood exceeds ''threshold''<br /> <br /> --minMapQuality ''threshold'' Positions where the root-means squared mapping quality falls below this threshold will be excluded.<br /> --minDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded.<br /> --maxDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded.<br /> --reference Positions called as homozygous reference will be included in the output.<br /> --uTsTv Use a uniform prior for transition-to-transversion ratio. <br /> <br /> To learn about default values for these options, simply run the program with no arguments.<br /> <br /> == Model for Variant Calling ==<br /> glfSingle uses a likelihood-based model for variant calling. Starting from genotype likelihoods ''Pr(reads| genotype)'' per genomic position, computed from appropriate tools (eg. Samtools BAQ), the likelihoods combine with an individual-based prior ''p(genotype)'' to generate posterior probabilities ''Pr(genotype| reads)''. <br /> <br /> Ingredients that go into prior:<br /> *All sites have an equal probability of showing polymorphism:<br /> **P(non-reference base) = 0.001<br /> *When a site shows polymorphism, it is usually heterozygous:<br /> **P(non-reference heterozygote) = 0.01 * 2/3<br /> **P(non-reference homozygote) = 0.01 * 1/3<br /> *Two options of mutation model:<br /> **Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account for minority of variants<br /> **Uniform prior for transition to transversion ratio (1:1)<br /> <br /> == Download ==<br /> <br /> For the current of glfSingle, please go to [http://www.sph.umich.edu/csg/abecasis/glfTools/ our GLF Tools Website].<br /> <br /> == TODO ==<br /> <br /> Support for X chromosome variant calling.<br /> <br /> Support for a two pass depth filter that uses the data to automatically work out appropriate filtering thresholds.</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=GlfSingle&diff=8703 GlfSingle 2013-09-23T19:17:41Z

<p>Yancylo: /* Model for Variant Calling */</p> <hr /> <div>[[Category:Software]]<br /> '''glfSingle''' is a [[GLF]]-based variant caller for next-generation sequencing data. It takes a [[GLF]] format genotype likelihood file as input and generates a [[VCF]]-format set of variant calls as output.<br /> <br /> == Basic Usage Example ==<br /> <br /> Here is an example of how <code>glfSingle</code> works:<br /> <br /> glfSingle -g NA19240.chrom20.SLX.glf -b NA19240.chrom20.SLX.vcf > NA19240.chrom20.SLX.log<br /> <br /> == Command Line Options ==<br /> <br /> -g ''genotype likelihood file'' Specifies the name of the input [[GLF]]-format genotype likelihood file<br /> -b ''base call file'' Specifies the name of the output [[VCF]]-format base call file<br /> -s ''sample label'' Specifies a label for the sample being analyzed, which will be included in the output VCF file<br /> -p ''threshold'' The threshold for base calling. Base calls will be made when their posterior likelihood exceeds ''threshold''<br /> <br /> --minMapQuality ''threshold'' Positions where the root-means squared mapping quality falls below this threshold will be excluded.<br /> --minDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded.<br /> --maxDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded.<br /> --reference Positions called as homozygous reference will be included in the output.<br /> <br /> To learn about default values for these options, simply run the program with no arguments.<br /> <br /> == Model for Variant Calling ==<br /> glfSingle uses a likelihood-based model for variant calling. Starting from genotype likelihoods ''Pr(reads| genotype)'' per genomic position, computed from appropriate tools (eg. Samtools BAQ), the likelihoods combine with an individual-based prior ''p(genotype)'' to generate posterior probabilities ''Pr(genotype| reads)''. <br /> <br /> Ingredients that go into prior:<br /> *All sites have an equal probability of showing polymorphism:<br /> **P(non-reference base) = 0.001<br /> *When a site shows polymorphism, it is usually heterozygous:<br /> **P(non-reference heterozygote) = 0.01 * 2/3<br /> **P(non-reference homozygote) = 0.01 * 1/3<br /> *Two options of mutation model:<br /> **Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account for minority of variants<br /> **Uniform prior for transition to transversion ratio (1:1)<br /> <br /> == Download ==<br /> <br /> For the current of glfSingle, please go to [http://www.sph.umich.edu/csg/abecasis/glfTools/ our GLF Tools Website].<br /> <br /> == TODO ==<br /> <br /> Support for X chromosome variant calling.<br /> <br /> Support for a two pass depth filter that uses the data to automatically work out appropriate filtering thresholds.</div>

Yancylo http://genome.sph.umich.edu/w/index.php?title=File:Scatterplot.png&diff=1362 File:Scatterplot.png 2010-05-19T14:14:32Z

<p>Yancylo: </p> <hr /> <div></div>

Yancylo