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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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query about PED and trio VCF #134

Closed prasundutta87 closed 2 years ago

prasundutta87 commented 2 years ago

Hi,

I have trio VCF for structural variants. The sequence of my samples in the VCF is Father, Mother. Proband. Does this sequence affect slivar results? I have seen slivar function in the form of kid, mom, dad.

I don't have a ped file. Do you have any recommendation on how to create one? Is vcftools okay to use like this:

vcftools --vcf <input_vcf> --out ped --plink

Regards, Prasun

brentp commented 2 years ago

you can just make text pedfile like this:

#family_id sample_id paternal_id maternal_id sex phenotype
1                kid_id        dad_id       mom_id        2    2
1                dad_id       0               0                   1     1
1                mom_id     0               0                   2      1

replacing mom_id, dad_id, and kid_id with the sample names in the VCF. Once you have this pedigree file, then the order of the samples doesn't matter, it just infers mom, dad and kid.

prasundutta87 commented 2 years ago

Thanks @brentp !