The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Did you remember to?

1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?

Then follow instructions in Article#1894.

Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

HaplotypeCaller and Allele balance issue

d_nid_ni Member Posts: 17

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

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,732 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 Member Posts: 17

    Hi Geraldine,

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


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



    300 x 1022 - 44K
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,732 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 Member Posts: 17

    Hi Geraldine,

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



  • GeraldineGeraldine BostonMember Posts: 4

    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 Member Posts: 17

    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.



Sign In or Register to comment.