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HaplotypeCaller missing SNP calls
I am in the process of validating the HaplotypeCaller in gatk3.8, and it is missing some obvious SNPs in GRCh37.
Playing around with various parameters I can make the variant being called or not. Most intriguing using the HaplotypeCaller with standard parameters but only change the region to be called from 22:50502363-50502727 to 22:50502413-50502727 two of the missing SNPs suddenly appears in the vcf file. Please see the two scenarios below I have included the bed regions in the screenshot: