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broadinstitute / gatk-sv

A structural variation pipeline for short-read sequencing
BSD 3-Clause "New" or "Revised" License
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Make the ploidy_table output a final output in JoinRawCalls #636

Closed kirtanav98 closed 1 month ago

kirtanav98 commented 5 months ago

The ploidy table is currently an intermediate output in JoinRawCalls. This file is required for further downstream analysis and is a necessary input for FilterGenotypes. Thus it should be a final output of the workflow. The JoinRawCalls wd. has been adjusted to make the ploidy table generated by calling CreatePloidyTableFromPed from the TasksClusterBatch.wdl a final output of the entire wdl. This passed validation with both womtool and cromshell against the reference panel.

kirtanav98 commented 1 month ago

This issues has been resolved.