Partitioned LD Scores

onlooker_zsq

已于 2022-09-21 15:54:44 修改

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于 2022-09-20 09:35:43 首次发布

本文链接：https://blog.csdn.net/onlookerq/article/details/126942824

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step1
for chrom in $(seq 22)
do
python make_annot.py \
  --bed-file ./baseline_v1.1/Conserved_LindbladToh.bed \
  --bimfile .//1000G_EUR_Phase3_plink/1000G.EUR.QC.$chrom.bim \
  --annot-file ./baseline/Conserved/Conserved.$chrom.annot.gz
done


step2
for chrom in $(seq 22)
do
./ldsc.py --l2 --bfile ./baseline/1000G_EUR_Phase3_plink/1000G.EUR.QC.$chrom --ld-wind-cm 1 --annot ./baseline/Conserved/Conserved.$chrom.annot.gz --out ./baseline/Conserved/Conserved.$chrom --print-snps ./baseline/hapmap3_snps/hm.$chrom.snp --thin-annot
done

下面就可以根据不能功能的ldscore计算

python ldsc.py --rg

Partitioned genetic correlation

https://storage.googleapis.com/broad-alkesgroup-public/LDSCORE/hapmap3_snps.tgz