UMAKE-glfSingle
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Jump to navigationJump to searchThis 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
Customization:
- 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");