Entering edit mode
9.4 years ago
vita.stepanova
•
0
Guys,
I have plink-format file with six individuals snps (.bed, .ped, .map) and want to convert it to classic bed (chr pos_start pos_end al1 al2 al1 al2 al1 al2 al1 al2 al1 al2 al1 al2
)
Do you know the best way?
Thanks in advance!
Thanks, but that brings me to file like
but I want to have
That's some strange hybrid of PLINK .tped and UCSC BED. Are you sure that is the format you want? What program/script do you need this for?
Actually, I wanted to split it into six files (according to individuals) and intersectbed them using bedtools
oh, I understand. what about generating a vcf file, and then extracting the genotypes through vcf-to-tab? that definitely would work, although I was trying to come out with a more elegant solution directly through plink.
Thanks for your replies! I have finally fixed it with tped.