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, 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 | + | 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 |
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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) |
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| ==Remarks== | | ==Remarks== |