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.
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.
Tranches plot issue
I think that this question has been asked before but I cannot find the way to fix the problem. I have just run VariantRecalibrator tool, and I'm getting this (see attached file) tranches plot for SNPs. I have understood correctly the tranches plot of the best practices manual but, I don't know what is going on here. I know that the tranches are sorted by Ti/Tv but for my, this plot makes no sense.
This is my command:
java -Xmx4g -jar GenomeAnalysisTK.jar \
-T VariantRecalibrator -R human_g1k_v37.fasta \
-input all.joinGeno.raw.vcf \
-resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.vcf \
-resource:omni,known=false,training=true,truth=true,prior=12.0 1000G_omni2.5.b37.vcf \
-resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.b37.vcf \
-resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.b37.vcf \
-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -mode SNP \
-tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 \
-recalFile recalibrate_SNP.recal \
-tranchesFile recalibrate_SNP.tranches \
Any help would be appreciated.