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.
VQSR for indels
I am running Variant Quality Score Recalibration on indels with the following command.
java -Xmx8g -jar /raid/software/src/GenomeAnalysisTK-1.6-9-g47df7bb/GenomeAnalysisTK.jar \ -T VariantRecalibrator \ -R /raid/references-and-indexes/hg19/bwa/hg19_lite.fa \ -input indel_output_all_chroms_combined.vcf \ --maxGaussians 4 -std 10.0 -percentBad 0.12 \ -resource:mills,known=true,training=true,truth=true,prior=12.0 /raid/Merlot/exome_pipeline_v1/ref/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf \ -an QD -an FS -an HaplotypeScore -an ReadPosRankSum \ --ts_filter_level 95.0 \ -mode INDEL \ -recalFile /raid2/projects/STFD/indel_output_7.recal \ -tranchesFile /raid2/projects/STFD/indel_output_7.tranches \ -rscriptFile /raid2/projects/STFD/indel_output_7.plots.R
My tranches file reports only false positives for all tranches. When I run VQSR on SNPS, the tranches have many true positives and look similar to other tranch files reported on this site. I am wondering if anyone has similar experiences or suggestions?