UMAKE-glfSingle - Revision history

Yancylo: /* Ingredients */

2014-01-22T16:32:25Z

Ingredients

← Older revision		Revision as of 12:32, 22 January 2014
Line 11:		Line 11:
	**An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.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:		**Note that the glfSingle and merging steps are included by enabling these two steps:
	RUN_PILEUP = TRUE # create GLF file from BAM then individual VCF using glfSingle		RUN_PILEUP = TRUE # create GLF file from BAM then individual VCF using glfSingle (sorry, you have to redo the pileups)
	RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls, population VCF by merging the glfSingle outputs		RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls, population VCF by merging the glfSingle outputs

Yancylo: /* Customization */

2014-01-22T16:30:05Z

Customization

← Older revision		Revision as of 12:30, 22 January 2014
Line 27:		Line 27:
	*To apply the uniform Ts/Tv model to glfSingle, go to the following line of umake-glfSingle.pl and make the changes in bold:		*To apply the uniform Ts/Tv model to glfSingle, go to the following line of umake-glfSingle.pl and make the changes in bold:
	**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");		**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");
	*To delete single-sample VCFs after merging, add the --d option to line 1000		*To delete single-sample VCFs after merging, add the --d option to line 1000 (do python merge_glfS_vcf.py to view option parameters)

	==Remarks==		==Remarks==

Yancylo at 16:29, 22 January 2014

2014-01-22T16:29:41Z

← Older revision		Revision as of 12:29, 22 January 2014
Line 27:		Line 27:
	*To apply the uniform Ts/Tv model to glfSingle, go to the following line of umake-glfSingle.pl and make the changes in bold:		*To apply the uniform Ts/Tv model to glfSingle, go to the following line of umake-glfSingle.pl and make the changes in bold:
	**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");		**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");
			*To delete single-sample VCFs after merging, add the --d option to line 1000

	==Remarks==		==Remarks==

Yancylo: /* Ingredients */

2014-01-15T21:51:43Z

Ingredients

← Older revision		Revision as of 17:51, 15 January 2014
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	*Perl script for generating Makefile		*Perl script for generating Makefile
	**Found at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl		**Found at /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)		**It is modified from umake.pl to use glfSingle and merge_glfS_vcf.py (for merging across single-sample VCF)
	***These two programs are available at /net/wonderland/home/yancylo/bin/umake-glfSingle		***These two programs are available at /net/wonderland/home/yancylo/bin/umake-glfSingle
	**To generate the Makefile corresponding to this new pipeline flow, do:		**To generate the Makefile corresponding to this new pipeline flow, do:

Yancylo: /* Ingredients */

2014-01-15T21:51:13Z

Ingredients

← Older revision		Revision as of 17:51, 15 January 2014
Line 4:		Line 4:

	==Ingredients==		==Ingredients==
	*Index file - same as original UMAKE index. An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.index		*Index file
	*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:		**same as original UMAKE index
			**An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.index
			*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:
	RUN_PILEUP = TRUE # create GLF file from BAM then individual VCF using glfSingle		RUN_PILEUP = TRUE # create GLF file from BAM then individual VCF using glfSingle
	RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls, population VCF by merging the glfSingle outputs		RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls, population VCF by merging the glfSingle outputs

	*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).		*Perl script for generating Makefile
	**These two programs are available at /net/wonderland/home/yancylo/bin/umake-glfSingle		**Found at /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)
			***These two programs are available at /net/wonderland/home/yancylo/bin/umake-glfSingle
	**To generate the Makefile corresponding to this new pipeline flow, do:		**To generate the Makefile corresponding to this new pipeline flow, do:
	perl /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl --conf /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf		perl /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl --conf /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf

Yancylo: /* Remarks */

2014-01-15T20:08:03Z

Remarks

← Older revision		Revision as of 16:08, 15 January 2014
Line 24:		Line 24:
	*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.		*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.
	*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.		*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.
	*One potential concern of this pipeline is ~~file~~ size, since each sample now has its own VCFs (~2Gb for chr20 per sample).		*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).

	==Contact==		==Contact==
	Please contact Yancy if you have any questions.		Please contact Yancy if you have any questions.

Yancylo at 20:07, 15 January 2014

2014-01-15T20:07:28Z

← Older revision		Revision as of 16:07, 15 January 2014
Line 3:		Line 3:
	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.		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.

	Ingredients:		==Ingredients==
	*Index file - same as original UMAKE index. An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.index		*Index file - same as original UMAKE index. An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.index
	*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:		*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:
Line 14:		Line 14:
	perl /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl --conf /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf		perl /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl --conf /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf

	Customization:		==Customization==
	*To change paths to glfSingle and merge_glfS_vcf.py, go to the following lines of umake-glfSingle.pl:		*To change paths to glfSingle and merge_glfS_vcf.py, go to the following lines of umake-glfSingle.pl:
	**line 1000 - my $cmd = "python [your-path]/merge_glfS_vcf.py --file-list $glfAlias --chr $chr --outfile $vcf > $vcf.log";		**line 1000 - my $cmd = "python [your-path]/merge_glfS_vcf.py --file-list $glfAlias --chr $chr --outfile $vcf > $vcf.log";
Line 20:		Line 20:
	*To apply the uniform Ts/Tv model to glfSingle, go to the following line of umake-glfSingle.pl and make the changes in bold:		*To apply the uniform Ts/Tv model to glfSingle, go to the following line of umake-glfSingle.pl and make the changes in bold:
	**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");		**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");

			==Remarks==
			*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.
			*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.
			*One potential concern of this pipeline is file size, since each sample now has its own VCFs (~2Gb for chr20 per sample).

			==Contact==
			Please contact Yancy if you have any questions.

Yancylo at 19:54, 15 January 2014

2014-01-15T19:54:15Z

← Older revision		Revision as of 15:54, 15 January 2014
Line 5:		Line 5:
	Ingredients:		Ingredients:
	*Index file - same as original UMAKE index. An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.index		*Index file - same as original UMAKE index. An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.index
	*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:		*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:
	RUN_PILEUP = TRUE # create GLF file from BAM then individual VCF using glfSingle		RUN_PILEUP = TRUE # create GLF file from BAM then individual VCF using glfSingle
	RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls, population VCF by merging the glfSingle outputs		RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls, population VCF by merging the glfSingle outputs

	*Perl script for generating Makefile - /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl . It is modified from umake.pl:		*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).
	**calls glfSingle and merge_glfS_vcf.py (for merging across single-sample VCF) ~~from~~ /net/wonderland/home/yancylo/bin/umake-glfSingle		**These two programs are available at /net/wonderland/home/yancylo/bin/umake-glfSingle
	**To generate the Makefile corresponding to this new pipeline flow, do:		**To generate the Makefile corresponding to this new pipeline flow, do:
	perl /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl --conf /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf		perl /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl --conf /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf

Yancylo at 19:49, 15 January 2014

2014-01-15T19:49:39Z

← Older revision		Revision as of 15:49, 15 January 2014
Line 13:		Line 13:
	**To generate the Makefile corresponding to this new pipeline flow, do:		**To generate the Makefile corresponding to this new pipeline flow, do:
	perl /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl --conf /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf		perl /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl --conf /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf
	**To change paths to glfSingle and merge_glfS_vcf.py, go to the following lines of umake-glfSingle.pl:
	***line 1000 - my $cmd = "python [your-path]/merge_glfS_vcf.py --file-list $glfAlias --chr $chr --outfile $vcf > $vcf.log";		Customization:
	***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");		*To change paths to glfSingle and merge_glfS_vcf.py, go to the following lines of umake-glfSingle.pl:
			**line 1000 - my $cmd = "python [your-path]/merge_glfS_vcf.py --file-list $glfAlias --chr $chr --outfile $vcf > $vcf.log";
			**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");
			*To apply the uniform Ts/Tv model to glfSingle, go to the following line of umake-glfSingle.pl and make the changes in bold:
			**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");

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, ..."

2014-01-15T19:46:44Z

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, ..."

New page

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, 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.

Ingredients:
*Index file - same as original UMAKE index. An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.index
*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:
RUN_PILEUP = TRUE # create GLF file from BAM then individual VCF using glfSingle
RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls, population VCF by merging the glfSingle outputs

*Perl script for generating Makefile - /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl . It is modified from umake.pl:
**calls glfSingle and merge_glfS_vcf.py (for merging across single-sample VCF) from /net/wonderland/home/yancylo/bin/umake-glfSingle
**To generate the Makefile corresponding to this new pipeline flow, do:
perl /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl --conf /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf
**To change paths to glfSingle and merge_glfS_vcf.py, go to the following lines of umake-glfSingle.pl:
***line 1000 - my $cmd = "python [your-path]/merge_glfS_vcf.py --file-list $glfAlias --chr $chr --outfile $vcf > $vcf.log";
***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");