The frontline support team will be offline as we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and available to answer questions on the forum on March 25th 2019.
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?