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nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
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Add target capture performance via Picard HsMetrics module #944

Open adamrtalbot opened 1 year ago

adamrtalbot commented 1 year ago

Description of feature

If we have a covered (by probes) and target file, we can use Picard's CollectHsMetrics for target sequencing performance.

Requires:

maxulysse commented 1 year ago

I think GATK_BEDTOINTERVALLIST should cover the BED part

FriederikeHanssen commented 1 year ago

I think GATK_BEDTOINTERVALLIST should cover the BED part

Probably just need to publishDir that process. Don't think we do that right now

FriederikeHanssen commented 1 year ago

the Hs Metric request has come up a few times. 🤞 it's in modules already and not a big thing to add :D