8000 mpileup on extremely high depth region · Issue #2293 · samtools/samtools · GitHub
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mpileup on extremely high depth region #2293

@gevro

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@gevro

Hi, samtools v1.20 mpileup on an extremely high depth region (> 100,000 reads) takes an extremely long time even when setting the -d (max depth) option to a very low number such as '10'. This doesn't make sense, since the first 10 reads from the region should be sufficient and output should be immediate.

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