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gatk FilterVariantTranches

jodybkjodybk LondonMember

I am a bit unsure on the usage of FilterVariantTranches. I have have applied CNNScoreVariants to a VCF and am now trying to filter. I am using another VCF as the resource (also after applying CNNScoreVariants) like this:

gatk FilterVariantTranches -V ERR1213935.CNN.vcf.gz --resource por7A1.CNN.vcf.gz --info-key CNN_1D --snp-tranche 99.95 --indel-tranche 99.4 -O out.vcf

However it is throwing the following error: A USER ERROR has occurred: VCF must contain SNPs and indels with scores and resources must contain matching SNPs and indels.

So my question does the overlap between the sample VCF and the resource have to be? At the moment they contain some of the same variants but also different ones. From the error message it seems like they should contain exactly the same variants?

Thanks in advance,
Jody

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