Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Missing reference allele in GVCF file after running HaplotypeCaller

astrandastrand New YorkMember
edited December 2014 in Ask the GATK team

Hi,

I used HaplotypeCaller in GVCF mode to generate a single sample GVCF, but when I checked my vcf file I see that the reference allele is not showing up:

22  1   .   N   <NON_REF>   .   .   END=16050022    GT:DP:GQ:MIN_DP:PL  0/0:0:0:0:0,0,0
 22 16050023    .   C   <NON_REF>   .   .   END=16050023    GT:DP:GQ:MIN_DP:PL  0/0:1:3:1:0,3,37
22  16050024    .   A   <NON_REF>   .   .   END=16050026    GT:DP:GQ:MIN_DP:PL  0/0:2:6:2:0,6,73
22  16050027    .   A   <NON_REF>   .   .   END=16050035    GT:DP:GQ:MIN_DP:PL  0/0:3:9:3:0,9,110
22  16050036    .   A   C,<NON_REF> 26.80   .   BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;MLEAC=1,0;MLEAF=0.500,0.00;MQ=27.00;MQ0=0;MQRankSum=-0.736;ReadPosRankSum=0.736 GT:AD:DP:GQ:PL:SB   0/1:1,2,0:3:23:55,0,23,58,29,86:1,0,2,0
22  16050037    .   G   <NON_REF>   .   .   END=16050037    GT:DP:GQ:MIN_DP:PL  0/0:3:9:3:0,9,109
22  16050038    .   A   <NON_REF>   .   .   END=16050039    GT:DP:GQ:MIN_DP:PL  0/0:4:12:4:0,12,153

I am not sure where to start troubleshooting for this, since all the steps prior to using HaplotypeCaller did not generate any obvious errors.

The basic command that I used was:
java -Xmx4g -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R hs37d5.fa -I recal_1.bam -o raw_1.vcf -L 22 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000

Have you encountered this problem before? Where should I start troubleshooting?

Thanks very much in advance,
Alva

Post edited by Geraldine_VdAuwera on

Comments

Sign In or Register to comment.