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[$NORMAL_NAME].AD[1] = 0
This filtered out all of the reads, although when I look at the VCF, there actually aren't any variants with a supporting read in the normal (all genotypes for the normal sample are 0/0). I then tried
isRef(GEN[Normal sample])
which also removed all variants. Lastly, I tried
countVariant() = 1
which seems to have done what I needed it to.
I manually added a variant with supporting reads in the normal sample, and only countVariant() = 1 performs as expected. These should all give the same output, assuming the VCF has 2 samples (normal and tumor) correct?
Thanks,
Yo
Hi developers,
I'm using SnpSift to filter a VCF that has an entries for variants in a tumor sample and a corresponding normal sample. I'm trying to filter out any variants that have a read that supports the variant in the normal sample, and first tried
GEN[$NORMAL_NAME].AD[1] = 0This 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() = 1which seems to have done what I needed it to.
I manually added a variant with supporting reads in the normal sample, and only
countVariant() = 1performs as expected. These should all give the same output, assuming the VCF has 2 samples (normal and tumor) correct?Thanks,
Yo