Changes

**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";

***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");

**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");