Entering edit mode
3.7 years ago
arctic
▴
40
Dear all, I am new to the field. I am trying to implement a GWA pipeline that recommends removal of "high linkage disequilibrium regions" prior to LD pruning. The pruned SNPs are then used for heterozygosity test and PCA of the subjects.
My questions are: 1. If removal of high LD regions is essential prior to LD pruning? 2. If yes, any advice on how to go about removing high LD regions for genotyping data with hg38 build is very much appreciated. I am unable to find the list of high LD regions for hg38.
Many thanks for your time and reply beforehand.
