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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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Processing data with unknown capture panel #3682

Open waemm opened 1 year ago

waemm commented 1 year ago

Hi,

This is more of a question I had some tumor-normal data run with an unknown capture panel. I assume I can run it whole genome but am concerned the variant detection and copy number estimates will be less accurate. Are there any tools in bcbio worth switching on to mitigate this ? Is it worth it to reverse engineer the capture through the BAM data?

Thanks!

naumenko-sa commented 1 year ago

Hi @waemm !

For the CNV analysis a bed file is necessary. WGS small variant calling mode could help deducing the panel - it should produce callable_regions.bed, i.e. regions of coverage.

SN