6c6e52def9
Reviewed pipelines with dev team. HSP updates: - Calling SNPs and Indels at the same time then using SelectVariants to separate them for filtering - Moved logs next to the files like in WGP - Flattened outputs into one directory - The file names for the final outputs are now <projectName>.vcf and <projectName>.eval - Updated test to pass the chr20 intervals instead of a boolean - Removed MultiFCP WGP updates: - Only cleaning and calling chromosomes 1-22, X, Y, MT - Splitting SNPs from indels, filtering indels, then merging the selected SNPs and selected Indels back together to make sure there are no collisions in CombineVariants - Still running VQSR on the recombined SNPs plus hard filtered indels - Using hard indel filters from delangel - Reduced number of tranches with rpoplin - Changed prior for dbsnp from 10 to 8 with rpoplin - Assuming identical samples on both CombineVariants - Explicitly using variant merge option UNION even though it's the default - Not setting the default genotype merge option PRIORITIZE - Generating a vcf and eval for each tranche git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5825 348d0f76-0448-11de-a6fe-93d51630548a |
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