SNP: low quality score filtering

epi2me-labs / wf-somatic-variation

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SNP: low quality score filtering #20

Closed selmapichot closed 2 months ago

selmapichot commented 2 months ago

Ask away!

Hi, when running the workflow for SNP, is it possible to set a threshold for clairS to filter out low quality variants ? Many thanks, Selma.

RenzoTale88 commented 2 months ago

Hi @selmapichot you can apply a soft filter on the QUAL value with the --min_qual option. The default value is currently set to 8. Please note that the variants are soft-filtered, meaning that the site will be in the VCF file, but with a FILTER tag set.