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HaplotypeCaller generate incorrect heterozygous Calls

nkausthunkausthu IndiaMember
edited August 29 in Ask the GATK team

Hi,
We have used GATK 3.6 and GATK 4.1 haplotype caller, to generate the variants, unfortunately, we are getting lots of incorrect heterozygous calls. Even only one read supports the variant it is considered as a heterozygous call. It would be great if someone can suggest what can be done in this scenario.

Chr Start End Ref Alt Zygosity Read frequency Read No Genotype Quality
1 27101249 27101249 - GGCGGGGCCCTGGGG Het 164,1 165 99
6 33141690 33141690 - GTAGGGTCCACGGGGTCAGCGGG Het 158,1 163 99
10 71906033 71906033 - G Het 150,9 160 91
11 66411384 66411384 C T Het 144,5 155 64
11 66411384 66411384 C T Het 144,5 155 64
17 79880575 79880575 G T Het 147,8 155 83
18 23807079 23807079 - ACTTTGGTCA Het 158,4 162 99
19 36276206 36276206 - GT Het 144,9 153 99
19 50340140 50340140 - GGGGGACCGGGCCCCGGGGA Het 154,3 157 99

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