I am not sure why HaplotypeCaller does not call my SNV mutation?
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Hi Guys, I am using HaplotypeCaller to call mutations for some of patient samples. I know that at MSH2 intron5 near splicing site there is a point mutation in one of the sample. however, this is also a region in Mills-1000g known indel file. Not matter how I try, Haplotypecaller can NOT call the SNV but always call the indel. the bam file is realigned and recalibrated using mills-1000g indel gold standard file. the position is chr2 47641560 the snapshot is attached. I am using 3.0 and gvcf mode on one single sample. notice there are 158X coverage at this position, 72 show allele base T, 72 are deletion. 84 show reference base A. mutect can easily pick it up though the reject reason is nearby-gap-event. Any input is highly appreciated. Thanks in advance.

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