Integrate ReshardVcf into ResolveComplexVariants #626
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epiercehoffman
approved these changes
May 28, 2024
| File contig_list | ||
| String prefix | ||
| Boolean? use_ssd | ||
| String sv_base_mini_docker | ||
| RuntimeAttr? runtime_override_reshard | ||
| } | ||
|
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| Array[String] contigs = read_lines(contig_list) | ||
| Array[String] contigs = transpose(read_tsv(contig_list))[0] |
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Make sure to update the ReshardVcf JSON templates (test & terra) to use the primary_contigs_fai to match this change - it looks like it was initially set up with primary_contigs_list
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It runs ok with the contigs list too
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Add json template Update top-level workflows; concat variant lists Fix contig list read Update ref panel outputs; fix CleanVcf template Fix Terra CleanVcf templates
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Adds a call to
ReshardVcfat the end ofResolveComplexVariants. In addition, each of theBOTHSIDES_PASSandHIGH_SR_BACKGROUNDcontig-sharded variant tables is concatenated into a single genome-wide table prior to annotating records with these flags inCleanVcf. This has a slight cost in memory footprint inCleanVcf1abut ensures that shuffled records are properly annotated. Json templates and top-level workflows are also updated.This branch was successfully tested on
ResolveComplexVariants,GenotypeComplexVariants,andCleanVcf.