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==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
RUN_PILEUP = TRUE # create GLF file from BAM then individual VCF using glfSingle
**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 (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
*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 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
**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 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 (do python merge_glfS_vcf.py to view option parameters)
==Remarks==
==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 --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.
