Haptyepecaller calls incorrect genotype in several site
I found that the Haptyepecaller made heterozygous calls where there is no support for them in the BAM. We use IGV to compare input BAM and Haptyepecaller output bam. The region shown in the figure confused us. At the top of this figure is input-BAM while another is Haptyepecaller-output-bam. Haptyepecaller-output-gvcf also suggest this site is heterozygous.
It seems that it's the same issue as https://gatkforums.broadinstitute.org/gatk/discussion/2319/haplotypecaller-incorrectly-making-heterozygous-calls-again. In that question,your suggested solution is updating GATK. Howerer,we used GATK 3.8 and GATK4.0.6 and we got same results.
The command line we used is:
~/software/gatk-220.127.116.11/gatk --java-options "-Xmx30G" HaplotypeCaller -L chr01:9550000-9850000 -ERC GVCF -R -I -O <output_g.vcf> -bamout