Question: extract SNPs (rs.....) along with subject ID and pedigree ID in PLINK
0
gravatar for pkpdkachroo
21 months ago by
Kiel, Germany
pkpdkachroo0 wrote:

Hi all,

I am trying to extract SNPs for a specific location with Pedigree ID information in there, however every time I use parameters, I get SNPs but without the pedigree or family ID. I want to merge SNPs with phenotype information using the common ID.

plink --bfile FULL_MERGE_chr17 --chr 17 --from-bp 39921041 --to-bp 39927601 --write-snplist --out FULL_MERGE_chr17.res

It produces a file which only has one column with all SNPs (FULL_MERGE_chr17.res.snpslist), however misses ID.

Could anyone suggest which parameter could be used to add ID information in the same SNP file?

I have tried adding --recode12 and --transpose, --recode-rlist but nothing seems to work! At some point, I got a different number of SNPs, but not all of them.

I would appreciate any help!

Thanks, Best, Priya

plink • 590 views
ADD COMMENTlink modified 21 months ago • written 21 months ago by pkpdkachroo0

Maybe just use --recode this gives you a .ped file and here the ID is next to the SNPs that are in your region

ADD REPLYlink written 21 months ago by Floris Brenk880
0
gravatar for pkpdkachroo
21 months ago by
Kiel, Germany
pkpdkachroo0 wrote:

Thanks, but I used that and as before my SNP file has 107 SNPs, but wc -l on the ped file gives me 2183. It does not look like I got the right ID.

ADD COMMENTlink written 21 months ago by pkpdkachroo0
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