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.
How to choose the right threshold for VariantRecalibrator
I am using VQSR on a non-model species (88 whole genomes, following strictly the GATK best practices). For that I use a database containing ~40000 SNPs, obtained by genotyping by sequencing on 150 different samples. And I do not know which prior I should use for it. For now my commands are:
java -Xmx120g -jar $GATK -T VariantRecalibrator
-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an DP -an InbreedingCoeff -mode SNP
Because I couldn't figure out which prior I should use, I tried 5, 10 and 20; here are the tranches plots. Note that I can't manage to obtain the other graphs (don't what is wrong with our R configuration on our server; I take any suggestion about it too).
Do you have any hint for me?