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HaplotypeCaller generate Calls is different when try to look the bam in IGV
I try to call SNP and use the gatk_126.96.36.199. When I check the result in IGV, the depth and result is different. Like that.
In IGV six samples on two site are both heterozygous, but in my result the three are homozygous. The depth of each site is also different.
Is there anything wrong ?
Thanks in advance!