Filtering variants with a supporting read in the normal sample

[yoakiyama]

Hi developers,

I'm using SnpSift to filter a VCF that has an entries for variants in a tumor sample and a corresponding normal sample. I'm trying to filter out any variants that have a read that supports the variant in the normal sample, and first tried

GEN[$NORMAL_NAME].AD[1] = 0

This filtered out all of the reads, although when I look at the VCF, there actually aren't any variants with a supporting read in the normal (all genotypes for the normal sample are 0/0). I then tried

isRef(GEN[Normal sample])

which also removed all variants. Lastly, I tried

countVariant() = 1

which seems to have done what I needed it to.

I manually added a variant with supporting reads in the normal sample, and only countVariant() = 1 performs as expected. These should all give the same output, assuming the VCF has 2 samples (normal and tumor) correct?

Thanks, Yo