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.
Hi GATK team,
I have a question about VQSR. For "VariantRecalibrator" I used as annotations: -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an InbreedingCoeff -mode SNP -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0; for "ApplyRecalibration" --ts_filter_level 99.0. I have an exome dataset of more than 200 samples but samples belong to at least 15 families. I wonder if I was wrong to use InbreedingCoeff as annotation and how much it could affect the final number of PASS variants.