Question: Using Plink to calculate LD between loci on different chromosomes
0
gravatar for jr.azaria
3.0 years ago by
jr.azaria0
jr.azaria0 wrote:

I'm trying to calculate LD between loci on different chromosomes using plink on the 1000 genomes vcf data. I plan on following this thread to convert my vcf files to bed and then merge all chromosomes into a single file: https://groups.google.com/forum/#!topic/plink2-users/RNztDLWCfB8 Then I plan on simply using the plink implementation from here to calculate LD: https://www.cog-genomics.org/plink/1.9/ld

Is there a simpler way to do this? Am I disregarding anything or doing something wrong?

snp plink ld • 1.3k views
ADD COMMENTlink written 3.0 years ago by jr.azaria0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 991 users visited in the last hour