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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?