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Input for VQSR from Mergevcfs

Dear GATK staff,

i have 28 vcf files from 31 humans exome data, the output after GenotypeGVCF according to the targeted gene intervals shows very little variant in each vcf files , less than 200 or 60 which seems might create a less reliable Gaussian model in VQSR. Should i use Mergevcfs to combine the 31 vcf files into a single file before piped them into VQSR?

Best Answer


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