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**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
*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:
*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==
