Add ReshardVcf workflow #613
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VJalili
reviewed
Oct 24, 2023
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| scatter (i in range(length(vcfs))) { | ||
| File vcf_indexes = vcfs[i] + ".tbi" | ||
| } |
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Would it be useful to add an optional input Array[File]? vcf_indexes and fall back to constructing the indexes based on the input VCFs if the optional input was not provided? I think it can be helpful to hint to a user if indexes are needed and provide them with an option of explicitly providing them (e.g., if they are on a different path).
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As a convention we always require input VCFs to have indexes for top-level workflows. These are already generated by the pipeline so shouldn't cause any problems as long as the VCFs were not manually moved without their indexes.
VJalili
approved these changes
Oct 24, 2023
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This workflow takes a set of vcfs and shards them by contig. The method uses
bcftools concatwith--regionsto pull records from all vcfs for each contig.This workflow will be needed at the end of
ResolveComplexVariants. This is because the contig-sharded vcfs produced in that workflow may contain a small number of records from other contigs, but downstreamCleanVcfrequires the input vcfs to be strictly contig sharded.Tested on reference panel outputs from
GenotypeComplexVariants.