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We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
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?