Post by anbai on Sept 1, 2021 12:36:49 GMT
Hello,
I was trying to compute the GRM using the imputed data from UKBB. My first approach is to follow the tuto here: cnsgenomics.com/software/gcta/#GREMLinWGSorimputeddata
But the first Step 1: segment based LD score, takes a long time, already 2 days. I merged all 22 autosomal chromosomes, in totoal, 8430655 SNPs passed the QC.
I also tried to run the tuto separately to each chromosome, but not sure if this is valid or not. Another post for this approach: www.biostars.org/p/362124/#9487305
Any suggestions for this? Thank you in advance
I was trying to compute the GRM using the imputed data from UKBB. My first approach is to follow the tuto here: cnsgenomics.com/software/gcta/#GREMLinWGSorimputeddata
But the first Step 1: segment based LD score, takes a long time, already 2 days. I merged all 22 autosomal chromosomes, in totoal, 8430655 SNPs passed the QC.
I also tried to run the tuto separately to each chromosome, but not sure if this is valid or not. Another post for this approach: www.biostars.org/p/362124/#9487305
Any suggestions for this? Thank you in advance