The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
GATK ClipReads option
I have a question concerning the ClipReads function and the different functionalities it's offering. The --clipRepresentation option and the different possibilites it offers doesn't seems to do what it's supposed to... As a matter of fact, I tried the REVERT_SOFTCLIPPED_BASES
and HARDCLIP_BASES options and those seem unefficient while giving in input bam files coming from bwa.
HARDCLIP_BASES seems to do what REVERT_SOFTCLIPPED_BASES is supposed to do. I end up using that as it's doing what I want. However, do you think it could be possible to add an option to change the base qualities of those bases that were reverted as we do not necessarily want to include them by using different BQ thresholds?
Thanks a lot!