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# HaplotypeCaller and Allele balance issue

Member

Hi Team!

I have an issue that I'm not sure how to solve.
I'm using HaplotypeCaller with a three member family and I have some calls when the HOM/HET call doesn't match with what we expected:

chr1 94487191 . A T 93.13 . AC=1;AF=0.167;AN=6;BaseQRankSum=-0.540;ClippingRankSum=-0.374;DP=87;FS=4.946;MLEAC=1;MLEAF=0.167;MQ=61.11;MQ0=0;MQRankSum=-0.042;QD=7.16;ReadPosRankSum=-0.042;set=GATK GT:AD:GQ:PL 0/0:40,0:99:0,102,2405 0/0:33,0:90:0,90,2215 0/1:11,2:99:124,0,760

In the third sample, the call is 0/1 (HET) but the coverage of each allele is 11 and 2, that means, with just 18% is considered as HET.
There is a way to change the Allele Balance to 30%?

The Genome Analysis Toolkit (GATK) v2.5-2-gf57256b, Compiled 2013/05/01 09:27:02

Program Args: -T HaplotypeCaller -R ucsc.hg19.fasta -I S1.bam -I S2.bam -I S3.bam -o OUT.RAW.vcf --genotyping_mode DISCOVERY -stand_call_conf 30.0 -stand_emit_conf 10.0

Tagged:

Hi there,

The genotype is determined based on the genotype likelihoods, not directly on the allele balance. Have you looked at the site in a browser such as IGV? This may tell you more about what's going on there; there may be low quality bases or mappings involved.

• Member

Hi Geraldine,

I was taking a look on IGV, here is the result:

For me, it still seems that is HOM... any tip?

Thanks!

Daniel.

Hi Daniel,

What are the base qualities for the reference reads? And have you looked at strand orientation for bias?

• Member

Hi Geraldine,

I attach a small sam file just with these region to see it by yourself with IGV.

Thanks,

Daniel.

• BostonMember

Daniel, I'm sorry but I don't have time to do an analysis for you. If you show me detailed evidence that GATK is doing the wrong thing then I can take a bug report, but until then it's up to you to do the legwork to collect that evidence.

• Member

It's ok Geraldine, you usually do more than enough to help us,

I'm not thinking that this is a bug, I just want to know if there are options that I can use to "configure" the genotype/allele balance or it's something that has no option to configure it.

Thanks!

Daniel.