To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

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

    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.

Sign In or Register to comment.