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?