SNP IDs changed when making .ped files using PLINK

Question

[kianalee]

I have data on genetic variants for multiple individuals for a family in the form of a .vcf file. I am successfully able to convert this .vcf file into a .ped file using plink:

plink --vcf  myvcf file --recode --out myplink

But when I read the .ped file into R and look at $genotype or $map, the SNPs are not named by either chromosomal location or an rs number, but are rather labeled "locus.1", "loucs.2", etc.

For example, in R:

>head(sample$map)

snp.name allele.1 allele.2
locus.1  locus.1        G        A
locus.2  locus.2        G        A
locus.3  locus.3        C        T
locus.4  locus.4        A     <NA>
locus.5  locus.5        C    CCCCT
locus.6  locus.6        T        G

How can I either trace back the actual genomic position of these loci, or make .ped files with either the chromosomal location or rs number?

Answer 1

[chrchang523]

If the chromosomal locations and rsIDs are in your VCF file, they'll also be in the .ped file generated by your plink command. I'd double-check how the R package works.