The frontline support team will be unavailable to answer questions until May27th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
HaplotypeCaller doesn't call true variants which are located on the outside of duplicated reads
I was running the haplotypeCaller for many samples, but some variants (validated as true positives by using other techniques) within these samples are not called by the haplotypeCaller. I saw in the bam files that most of these variants are located on the outside of duplicated reads (around 200 reads). Most of my data consists of duplicated reads. First I thought that the duplicated reads were filtered out by the read filters which are automatically applied (like duplicateReadFilter), but when I checked it this was not the case. I was wondering why my true variants are not called by the HaplotypeCaller and if there is an option to resolve this problem?