Changes

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