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variants filtering VQSR

jfjfjfjf Member
edited October 2015 in Ask the GATK team

Hi,

I ran VQSR with 30 samples and tranche filter level of 99.0 for both SNPs and INDELs. Around 82% of my variants call pass the filter. May I know is there any standard that can be used to evaluate how good the filtering result is?

Besides, if I split the gvcfs by chromosomes and run joint genotyping (GenotypeGVCFs) at chromosome level, is it going to affect the result compared to running at whole genome level?

Thanks,
jf

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