I used HaplotypeCaller for variant calling out of WES picard.sorted.MarkedDup.bam file with GATK 4.2.6.1. HaplotypeCaller standard command line.
Apparently, everything worked well and I received standard .vcf file. But the number of identified variants are too much for WES result. It's close to one million variants for one sample! Did I perform something wrong? What solution do you recommend? Any help would be appreciated.
The command line I used was as follow:
gatk --java-options -Xmx8g HaplotypeCaller \ -R $refFile \ -I ${base}.picard.sorted.markedDup.bam \ --dont-use-soft-clipped-bases -stand-call-conf 20.0 \ --emit-ref-confidence GVCF \ -O ${base}.rrrrealigned.vcf