Hi,
I'm having a confusing problem when using haplotypecaller.
Basically, I'm using haplotypecaller calling variants among more than 400 M. tuberculosis samples, sequenced with Hiseq2500 platform. I followed the workflow for calling variants on cohort samples as described here: https://gatkforums.broadinstitute.org/gatk/discussion/3893/calling-variants-on-cohorts-of-samples-using-the-haplotypecaller-in-gvcf-mode
I find a problem with some samples when checking the SNPs called by this procedure. For example, as in Sample1, as show in this figure 
,there seems to be a deletion at the position 2866805. However, the GATK3.8 called a SNP at this position, as shown in the excerpt from the vcf file below:
NC_000962.3 2866805 . C G 8160 . AC=1;AF=1.00;AN=1;DP=182;FS=0.000;GQ_MEAN=8190.00;MLEAC=1;MLEAF=1.00;MQ=50.38;MQ0=0;NCC=0;QD=31.09;SOR=0.917 GT:AD:GQ:PL 1:0,176:99:8190,0
In total, haplotypecaller called 11 snps at this deletion region.
So I'm confused that why haplotypecaller called a snp variant when bam file shows there is a deletion? I would really appreciate if you could help me to figure this out. Thank you in advance!
P.S. after finding this problem, we also tried UnifiedGenotyper on Sample1, and the variants at the deletion region were not called this time.