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170 bytes added ,  12:32, 22 January 2014
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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
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   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:
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*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==
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