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.
SOR annotation related error from VariantRecalibrator
I am getting this error from variant recalibrator:
ERROR MESSAGE: Bad input: Values for SOR annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations
Does this mean I have to bring these in from external resources --- dbSNP? I thought haplotypecaller should bring these tags.
This is what the format haplotypeCaller has produced. There is no SOR annotation. I am working with a single whole genome.
1 14590 . G A 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.282;ClippingRankSum=-0.592;DP=13;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=25.74;MQ0=0;MQRankSum=-1.268;QD=5.21;ReadPosRankSum=-1.268 GT:AD:DP:GQ:PL 0/1:10,3:13:96:96,0,411