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181 bytes added
, 12:32, 22 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 | + | *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: | + | **same as original UMAKE index |
− | RUN_PILEUP = TRUE # create GLF file from BAM then individual VCF using glfSingle | + | **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 included by enabling these two steps: |
| + | 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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− | *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). | + | *Perl script for generating Makefile |
− | **These two programs are available at /net/wonderland/home/yancylo/bin/umake-glfSingle | + | **Found at /net/wonderland/home/yancylo/bin/umake-glfSingle/umake-glfSingle.pl |
| + | **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 |
| **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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| *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== |