Hello, I have a feature request:
I've identified samples where average depth wasn't enough to filter out cases where HLA genes were sequenced poorly at specific exons. In particular, a subset of samples where half of HLA-A was sequenced at 10x and the other half at 30x, resulting in poor quality; however applying average coverage as a quality metric did not filter these out or flag this issue. Do you have any recommendations for a metric that could catch this or would it be possible to add an additional metric such as "% positions covered at X depth"?
Thanks!
Hello, I have a feature request: I've identified samples where average depth wasn't enough to filter out cases where HLA genes were sequenced poorly at specific exons. In particular, a subset of samples where half of HLA-A was sequenced at 10x and the other half at 30x, resulting in poor quality; however applying average coverage as a quality metric did not filter these out or flag this issue. Do you have any recommendations for a metric that could catch this or would it be possible to add an additional metric such as "% positions covered at X depth"? Thanks!