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set=FilteredInAll from CombineVariants not actually in all input VCFs

I'm using GATK CombineVariants to combine multiple VCFs. According to this page, set=filteredInAll means "occurred in both call sets, but was filtered out of both". Unfortunately, I have VCFs where only 1 of the 3 VCFs has the variant, but it's still annotating set=filteredInAll, which is misleading.

If you run grep 71983 over the attached VCFs, you will note that only the VarDict VCF contains a variant at position chr19:71983.

However, after combining the VCFs with the following command I get set=FilteredInAll for this position:

gatk -T CombineVariants --downsampling_type NONE  --variant:MuTect2 TCRBOA3.MuTect2.vcf  --variant:mutect TCRBOA3.mutect.vcf  --variant:VarDict TCRBOA3.vardict.vcf -priority MuTect2,VarDict,mutect -R ucsc.hg19.fasta --genotypemergeoption PRIORITIZE  -o combined.vcf

(you'll need the reference genome and to rename the uploaded files to .vcf for this command to work)

Is this wrong? Or am I misunderstanding the results?

Answers

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