Hi, I've been noticing that my median deduplicated depth goes up after sub-sampling (with samtools view -s) compared to the original median depth. Wondering if anyone else has observed something similar and if it's an artifact of samtools view -s? I don't think it is an issue with picking the same seed in multiple sequential sub-samplings because the original bam that is being sampled from was not already sub-sampled previously.
My workflow is:
complete non-deduped bam file -> sub-sample or no sub-sampling -> barcode deduplication -> calculate median depth
My workflow is:
complete non-deduped bam file -> sub-sample or no sub-sampling -> barcode deduplication -> calculate median depth
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