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.
Indel Variant recalibration is showing an error
I have done joint genotyping of 200 samples and I have a multi sample vcf file. SNP recalibration worked but when I did Indel quality score recalibration it shows an error "MESSAGE: Bad input: Values for QD annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations"
I have used the below command
java -Xmx8g -XX:ParallelGCThreads=20 -jar /mnt/exome/Softwares/GenomeAnalysisTK.jar -T VariantRecalibrator -R /mnt/exome/ReferenceFiles/human_g1k_v37.fasta -input recalibrated_snps_raw_indels.vcf -resource:mills,known=true,training=true,truth=true,prior=12.0 /mnt/exome/ReferenceFiles/Resource/Mills_and_1000G_gold_standard.indels.b37.vcf -an QD -an DP -an FS -an SOR -an ReadPosRankSum -an MQRankSum -mode INDEL -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 --maxGaussians 4 -recalFile recalibrate_INDEL.recal -tranchesFile recalibrate_INDEL.tranches -rscriptFile recalibrate_INDEL_plots.R
It would be really great if some one can help me to trouble shoot this.