Downsample process in ActiveRegion determination (HaplotypeCaller and Mutect2)
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14 months ago
yxwucq • 0

https://gatk.broadinstitute.org/hc/en-us/articles/360036227652?id=4147

In the article it described the process of finding active regions. I found Downsampling step in final post-processing quite confusing. Could someone explain the reason for this step?

There is a final post-processing step to clean up and trim the ActiveRegion:

Downsample remaining reads to a maximum of 1000 reads per sample, but respecting a minimum of 5 reads starting per position. This is performed after any downsampling by the traversal itself (-dt, -dfrac, -dcov etc.) and cannot be overriden from the command line.

Downsample Mutect2 HaplotypeCaller • 344 views
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