This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
Prevent haplotypecaller from using soft-clipped proportion of the read
Dear GATK team,
From what I read on the forum, it seems that HaplotypeCaller call variants (and perhaps calculates RGQ) using soft-clipped parts of the reads? Is there a parameter to suppress this behavior, making it throw out the soft-clipped proportions before calling?