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