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.

HaplotypeCaller filter option

my script:
java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R reference.fa -filterRNC -filterMBQ -filterNoBases -rf UnmappedRead -rf BadMate -rf DuplicateRead -rf NotPrimaryAlignment -rf MappingQualityUnavailable -recoverDanglingHeads -dontUseSoftClippedBases -stand_call_conf 20 -stand_emit_conf 20 -o WT.vcf -I WT.bam

there is some strange results in VCF, such as:
Unigene0001766 300 . T C 7075.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-3.715;ClippingRankSum=-0.042;DP=236;FS=5.542;MLEAC=2;MLEAF=1.00;MQ=50.00;MQ0=0;MQRankSum=0.228;QD=29.98;ReadPosRankSum=-3.631 GT:AD:DP:GQ:PL **1/1:14,222**:236:99:7104,131,0

this is likely use default option to determin genotype, why not 0/1?
I didn`t see any options to control it.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    In its current implementation, the program expects diploid proportions by default, so such a skewed ratio can not be called 0/1 since it diverges too far from 50:50 ratio. If this is RNAseq and you think this could be a case of differential allele expression (which you would need a DNAseq control to support), then we may have a new tool in the next version that will be able to interpret this correctly. But it is not yet ready.

Sign In or Register to comment.