GATK FilterVariantTranches - all mutations passed the filter

Question

[Vladislav]

Hi, Biostars community.

I tried to filter variants in my .vcf file using GATK CNNScoreVariants and FilterVariantTranches, but in result file all mutations passed the filter.

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Commands:

gatk CNNScoreVariants -V input.vcf -R reference.fa -O scored.vcf

gatk FilterVariantTranches -V scored.vcf \
   --resource hapmap_3.3.hg38.scored.vcf \
   --resource Mills_and_1000G_gold_standard.indels.hg38.scored.vcf \
   --info-key CNN_1D \
   -O result.vcf

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Addictional info:

• GATK version: 4.1.8.0
• OS: Ubuntu Server 18.04
• All commands executed under GATK conda enviroment.
• Resource vcf files scored via CNNScoreVariants.

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Solved

Solved via specifying "-snp-tranche" and "-indel-tranche" options.

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