LD Score Regression in Single Cells
You have to be careful with naming conventions else the the software will bark at you
python munge_sumstats.py --sumstats sumstats/cd.u.txt --N 27726 --merge-alleles sumstats/w_hm3.snplist --out sumstats/CROHN --a1-inc
python ldsc.py --l2 --bfile 1000G_EUR_Phase3_plink/1000G.EUR.QC.22 --ld-wind-cm 1 --print-snps list.txt --annot hemeBulk/heme22.annot --out hemeBulk/heme22
python ldsc.py --h2 sumstats/BMI.sumstats.gz --ref-ld-chr hemeBulk/heme --overlap-annot --w-ld-chr weights_hm3_no_hla/weights. --frqfile-chr 1000G_Phase3_frq/1000G.EUR.QC. --out BMI_baseline
bsub -q big -M 64000 -R 'rusage[mem=64000]' python ldsc.py --h2 sumstats/BMI.sumstats.gz --ref-ld-chr scMyeloid/scHeme --overlap-annot --w-ld-chr weights_hm3_no_hla/weights. --frqfile-chr 1000G_Phase3_frq/1000G.EUR.QC. --out scMyeloid/BMI
The raw.annot folder contains annotation files for 1000 Genomes Project. Here's what the first few lines look like--
zcat < ../raw.annot/raw.1.annot.gz | head -5
CHR BP SNP CM base
1 11008 rs575272151 0.0 1
1 11012 rs544419019 0.0 1
1 13110 rs540538026 0.0 1
1 13116 rs62635286 0.0 1
What one would want to do for another set of data is take the annotation files and use awk
to make similar files and then plug and chug the key Rscript code/bed2annotate.R