If I get it right, anomalous read pairs refer to those where only one read is mapped. I wonder whether GATK would ever use these reads to do the calling.
Yes, the HaplotypeCaller will try to use reads even if their mate is unmapped. To disable this behavior, you can use the BadMate filter.
You can read more about which read filters are applied by HC here: https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php
Hi @Geraldine_VdAuwera ,
Thank you very much for the quick response! But I when check the available read filters are listed in the online tool documentation, I thought that maybe MateSameStrand filter would be a better choice for my situation?
You're correct, MateSameStrand is indeed more appropriate in your case, my mistake.