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SciLifeLab / Sarek

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
https://nf-co.re/sarek
MIT License
133 stars 7 forks source link

Target Coverage in BAMQC #670

Closed apeltzer closed 4 years ago

apeltzer commented 6 years ago

Is your feature request related to a problem? Please describe.

The target coverage is computed in BAMQC based on the entire genome. For exome data (even with specified BED file and therefore regions, Sarek doesn't specify the coverage on covered sites but instead the overall coverage on the entire genome.

Describe the solution you'd like

Use the --gff switch in QualiMap2 to run with the specified BED file. That provides more accurate coverage on target capture coverage.

szilvajuhos commented 5 years ago

Cool, other groups were also requesting something similar, I already made some prototype, we can also add the QualiMap2 part. Will work on that.

apeltzer commented 5 years ago

Just make sure to use a more updated QualiMap2 version. The possibility to use BED-3 instead of BED-6 format, was just introduced fairly recently (upon my request... https://bitbucket.org/kokonech/qualimap/commits/all ). I don#t know which version of QualiMap2 is shipped with the current Sarek container(s), so we should make sure that this works :-)

maxulysse commented 4 years ago

Transferred to the new nf-core/sarek repo