8000 samtools markdup memory usage on high-depth regions · Issue #2296 · samtools/samtools · GitHub
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samtools markdup memory usage on high-depth regions #2296

@daviesrob

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@daviesrob

samtools 1.22.1

When markdup hits high-depth regions, it can use a lot of memory as it keeps hold of all records overlapping the current one. On a particularly bad input we have, where the depth was over 120 million, this caused processing to fail due to running out of memory. The problematic region has been extracted from this for testing purposes and will be shared separately.

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