Issues have appeared in production where bcftools_quality_filter_svdb fails due to a float-value of CN from cnvpytor. This has been resolved in production manually by either rounding up or down the CN value, or by changing the header of the VCF:
From:
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
To:
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
Production should not need to do this manual work and the fix should be easy.
Suggested approach
Add something like this:
sed 's/FORMAT=<ID=CN,Number=1,Type=Integer/FORMAT=<ID=CN,Number=1,Type=Float/g' -i {params.tmpdir}/{params.tumor}.vcf
To the cnvpytor rule.
Considered alternatives
Rounding up or down the float should not be the recommended approach if simply modifying the header solves the issue.
Requests/suggestions/bugs solved by the feature
Duplicate issues have been created from production:
mathiasbio
commented
1 year ago
Need
Issues have appeared in production where bcftools_quality_filter_svdb fails due to a float-value of CN from cnvpytor. This has been resolved in production manually by either rounding up or down the CN value, or by changing the header of the VCF:
From:
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">To:##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">Production should not need to do this manual work and the fix should be easy.
Suggested approach
Add something like this:
sed 's/FORMAT=<ID=CN,Number=1,Type=Integer/FORMAT=<ID=CN,Number=1,Type=Float/g' -i {params.tmpdir}/{params.tumor}.vcfTo the cnvpytor rule.Considered alternatives
Rounding up or down the float should not be the recommended approach if simply modifying the header solves the issue.
Requests/suggestions/bugs solved by the feature
Duplicate issues have been created from production:
Can be closed when
Blockers
Anything preventing this from happening?
Validation/Verification suggestion