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Incorrect Heterozygotic Call

bralhabralha CanadaMember
edited March 2015 in Ask the GATK team

Hello GATK Team,

I've just run the following using GATK v3.1.

gatk -R ref.fa -T UnifiedGenotyper -I Q11_Final.sorted.rg.bam -I Q11D1.sorted.bam -I Q11D4.sorted.bam -I Q11D2.sorted.bam -I Q11D5.sorted.bam -o PX.raw.vcf -nt 5 -glm SNP -ploidy 2

I then trimmed SNPs within 10bp of indels (called using the same but -glm indel).

The samples therein represent a mother (Sample Q11) and her 4 haploid sons.

The problem I'm getting is that calls that should be heterozygotic in the mother are not being called as such (see attached image; .bam file of the mother is int he bottom and the resulting VCF file is loaded in the top panel. The green cmd screen shows the VCF file line for the site in question where the 14th element of the indicates the queen's results (1/1:68,86:154:99:1837,120,0)

I'm not sure what's going on here and was wondering if you could help out?


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @bralha ,

    It looks like the call is a little ambiguous, it's possible that some read biases pushed it over the line to hom-var. Have you tried running HaplotypeCaller instead of UG on the region? It is a much more advanced tool than UG. You can also try our genotype refinement workflow. Our primary tools are geared toward producing highly accurate variant calls (in the sense of detecting variation) but the genotype determination (between het and hom-var) can be further refined.

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