HaplotypeCaller and Allele balance issue

d_nid_ni Posts: 17Member

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%?

More info:

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

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,973Administrator, GATK Developer admin

    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.

    Geraldine Van der Auwera, PhD

  • d_nid_ni Posts: 17Member

    Hi Geraldine,

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

    image

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

    Thanks!

    Daniel.

    IGV.jpg
    300 x 1022 - 44K
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,973Administrator, GATK Developer admin

    Hi Daniel,

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

    Geraldine Van der Auwera, PhD

  • d_nid_ni Posts: 17Member

    Hi Geraldine,

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

    Thanks,

    Daniel.

    zip
    zip
    test.sam.zip
    2K
  • GeraldineGeraldine BostonPosts: 4Member

    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.

  • d_nid_ni Posts: 17Member

    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.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,973Administrator, GATK Developer admin

    Oh, I see. No, that's not something you can tweak from command line.

    Geraldine Van der Auwera, PhD

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