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epi2me-labs / wf-human-variation

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cannot detect snv with adaptive sampling #173

Closed dhlee3342 closed 2 months ago

dhlee3342 commented 2 months ago

Ask away!

Hi,

I used wf-human-variation to detect snp in my genes of interest with adaptive sampling. Most mutations were normally detected, but some mutations were not detected, in one bed region. When I checked the bam file with IGV, there's a low coverage groove in the region that mutations were not detected. Roughly, the reads number is lower than 20. Question is, If there is a low depth region in one bed area, does the caller skip only that part?

Thank you.

dhlee3342 commented 2 months ago

Hi,

I found all the variants with --bam_min_coverage 10 option. I think I knew the mechanism.

Thank you.

vlshesketh commented 2 months ago

Hi @dhlee3342, thanks for your interest in the workflow. As you have identified the parameter required, I'll close this issue, but please don't hesitate to get in touch again in the future if you have any other questions.