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We have 100 samples run through the GATK unified genotyper and then we merged all the VCF files to run the multi samples VQSR. (merged was done using VCFTOOLS). What attributes we should use in this case.
For multi sample called vcf we use these paramters:
-an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an MQ -an DP -nt 2 --maxGaussians 4 --percentBadVariants 0.05
any help is deeply appreciated.