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HaplotypeCaller generate Calls is different when try to look the bam in IGV

TomliuTomliu Member
edited October 2019 in Ask the GATK team

I try to call SNP and use the gatk_4.1.0.0. 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!
Best wishes,
Yu Liu



  • bshifawbshifaw Member, Broadie, Moderator admin

    Hi Yu,

    Please try rerunning with GATK4.1.4.0, if the problem continues please attach the command that was used, the java version of the system, and a snippet of the data as described in this article

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