SNP IDs changed when making .ped files using PLINK
Entering edit mode
2.1 years ago
kianalee • 0

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) 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?

plink SNP • 514 views
Entering edit mode
2.1 years ago

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.


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