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11 bytes added ,  17:51, 15 January 2014
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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
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*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:
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**same as original UMAKE index
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**An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.index
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*Configuration file
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**same as original UMAKE conf
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**An example is at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.conf
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**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 to call glfSingle and merge_glfS_vcf.py (for merging across single-sample VCF).
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*Perl script for generating Makefile
**These two programs are available at /net/wonderland/home/yancylo/bin/umake-glfSingle
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**Found at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl
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**It is modified from umake.pl to call glfSingle and merge_glfS_vcf.py (for merging across single-sample VCF)
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***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
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