Remove CHR2 and END2 from INS in CleanVcf - Githubissues

broadinstitute / gatk-sv

A structural variation pipeline for short-read sequencing

BSD 3-Clause "New" or "Revised" License

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Remove CHR2 and END2 from INS in CleanVcf #631

Closed epiercehoffman closed 2 months ago

epiercehoffman commented 5 months ago

Updates

Remove CHR2 and END2 from INS in CleanVcf. In most cases, these fields duplicate information in CHROM and POS. In other cases, they duplicate information in SOURCE. The inconsistent use is confusing and unnecessary.
Do not require CHR2 in svtk. If CHR2 is not present, use CHR2=CHROM. This was causing issues when running svtk vcfcluster after removing CHR2 from INS.

Testing

Built updated docker image, ran CleanVcf, and verified CHR2 and END2 tags were not present in INS records
Ran reclustering workflow with updated docker image and it resolved the error message about CHR2<CHROM and the subsequent error message about the missing CHR2 field
Validated all WDLs and JSONs with womtool and Terra validation script

epiercehoffman commented 2 months ago

We've been rolling with this for a while now so I'd assume it's okay still. Did it cause any issues with CPX records for other downstream workflows like ManualReview?

We had to update ManualReview to accommodate #583. I don't recall any additional issues that arose as a result of altering the INS records (this PR). The issues we had with that were related to reclustering, and I addressed those as part of this PR.