group expr results

[snashraf]

Hi Brent,

I am running an expression like below.

./slivar expr --vcf sample_merged_denovo_SIZEGT300_SETGT.vcf --ped family.ped --out-vcf temp.vcf --group-expr "denovo:kida.alts != 0 && kidb.alts != 0 && mom.alts == 0 && dad.alts == 0 && sibling.alts == 0 " --alias sliver.group

where I am trying to look for denovo variants and both kida and kidb are sick while siblings is a healthy.

when I am looking into the output vcf (attached ) file then I am getting the below lines. I simply want to get all denovo SV which is not present in Mom, dad and Siblings and present in kida and Kidb but for some reason, I am not getting the correct output. Could you please look into this? I am attaching ped file and group file as well.

family.ped.txt slivar.group.txt

forpostatgithub.vcf.txt

[brentp]

remember to use --pass-only if you only want variants that pass. I do:

slivar expr --vcf forpostatgithub.vcf.txt --out-vcf temp.vcf --group-expr "de:kida.alts != 0 && kidb.alts != 0 && mom.alts == 0 && dad.alts == 0 && sibling.alts == 0 " --alias slivar.group.txt --pass-only
> slivar version: 0.2.2 0401ef029e3b2dee542c56c35d1dae3a8c245dfb
[slivar] 5 samples matched in VCF and PED to be evaluated
[slivar] Finished. evaluated 10 total variants and wrote 0 variants that passed your slivar expressions.
sample  de
ORVA_0200741981 0
ORSE_0200741991 0
ORAN_0200742001 0
CUGR_0200742011 0
ORMA_0200742021 0

and get no variants matching.

I suspect the denovo= tags in the VCF you added are from a previous (incorrect) version of your expression. Note that slivar will not remove a pre-existing denovo field from the INFO if the expression does not pass; might be good to add a message about this but meanwhile, let me know if this resolves your issue. -Brent

[snashraf]

Thanks !! yes, it worked. You are correct as this "denovo" was from earlier and incorrect run.