Family ID in PED file

Question

[iferrazamaro]

Hi,

I have a PED file with Individual IDs but not Family IDs. I want to add the Family IDs (it would be ok for me having the same ID as Individuals) in my PED file. I have been using, for this, --update-ids but it does not work. How could I do this?

Thanks. Ivan.

[rajneeshpaliwal]

Dear Ivan,

I have same issue. Did you get any solution. I will be happy if you or any Booster member help me to solve it.

Regards Rajneesh

Answer 1

[natasha.sernova]

See this post:

A: Simple Question About .Ped Format For Gatk And Plink

And this file-format reference:

https://www.cog-genomics.org/plink2/formats

I took just two paragraphs:

.clst (cluster membership file)

Produced by --write-cluster. Valid input for --within.

A text file with no header line, and one line per sample with the following three fields: 1. Family ID 2. Within-family ID 3. Cluster name

.genome (identity-by-descent report)

Produced by --genome. Valid input for --read-genome.

A text file with a header line, and one line per pair of distinct samples typically with the following 14 fields: FID1 First sample's family ID IID1 First sample's within-family ID FID2 Second sample's family ID IID2 Second sample's within-family ID RT Relationship type inferred from .fam/.ped file EZ IBD sharing expected value, based on just .fam/.ped relationship Z0 P(IBD=0) Z1 P(IBD=1) Z2 P(IBD=2) PI_HAT Proportion IBD, i.e. P(IBD=2) + 0.5P(IBD=1) PHE Pairwise phenotypic code (1, 0, -1 = case-case, case-ctrl, and ctrl-ctrl pairs, respectively) DST IBS distance, i.e. (IBS2 + 0.5IBS1) / (IBS0 + IBS1 + IBS2) PPC IBS binomial test RATIO HETHET : IBS0 SNP ratio (expected value 2)

This link mat be useful:

http://www.shapeit.fr/pages/m02_formats/pedmap.html

Answer 2

[chrchang523]

Use --no-fid to tell plink that there is no separate Family ID column in the input file. In this case, plink will set the Family ID to be equal to the Individual ID, and --recode will generate a .ped file with both columns.