Hi,
I'm trying to calculate LD scores for non-European population using 1000 Genome Phase 3 data.
Therefore, I tried to estimate the LD Scores in European as a pilot.
I started from 1000 Genome Project Phase 3 vcf file and converted into plink formats. I compared the one I converted from vcf with the provided plink file, 1000G_Phase3_plinkfiles.tgz . I find there are much much less variants (about 1/3 of the variants in the vcf file) in the plink file provided by your team. I'm wondering is there any other quality control you set up for the conversion?
@bulik @hilaryfinucane
Best,
Siwei
Hi,
I'm trying to calculate LD scores for non-European population using 1000 Genome Phase 3 data.
Therefore, I tried to estimate the LD Scores in European as a pilot.
I started from 1000 Genome Project Phase 3 vcf file and converted into plink formats. I compared the one I converted from vcf with the provided plink file, 1000G_Phase3_plinkfiles.tgz . I find there are much much less variants (about 1/3 of the variants in the vcf file) in the plink file provided by your team. I'm wondering is there any other quality control you set up for the conversion?
@bulik @hilaryfinucane
Best,
Siwei