msarguru
commented
4 weeks ago Update. Got this sorted, turned out issue with the filenaming.. also few suggestions on the readme for git.. one has to use git sparse-checkout set --no-cone * to get all the required ldscore files.
Would love an addition on the interpretation of the output.. what each column refers to, etc. Thanks again
Hi, thank you for the iLDSC. Trying it on a sumstat.gz that works for LDSC, returns the index out of range error. and I am using the following syntax. Any suggestions, would be greatly appreciated. ./ldsc.py \ --h2 ../sumstats/PSS.EUR.pdt10.nomerge.sumstats.gz \ --ref-ld-chr ./EUR_1000G/Full_cisLD/ \ --out WMH_EUR_ildsc \ --w-ld-chr ../ldsc/eur_w_ld_chr/ \ --print-coefficients
Beginning analysis at Wed Aug 14 20:19:44 2024 Reading summary statistics from ../sumstats/PSS.EUR.pdt10.nomerge.sumstats.gz ... Read summary statistics for 5355832 SNPs. Reading reference panel LD Score from ./EUR_1000G/Full_cisLD/[1-22] ... (ldscore_fromlist) Traceback (most recent call last): File "ildsc.py", line 651, in
sumstats.estimate_h2(args, log)
File "/annotation/ldsc-F/ildsc/ldscore/sumstats.py", line 329, in estimate_h2
args, log, args.h2)
File "/annotation/ldsc-F/ildsc/ldscore/sumstats.py", line 245, in _read_ld_sumstats
ref_ld = _read_ref_ld(args, log)
File "/annotation/ldsc-F/ildsc/ldscore/sumstats.py", line 82, in _read_ref_ld
'reference panel LD Score', ps.ldscore_fromlist)
File "/annotation/ldsc-F/ildsc/ldscore/sumstats.py", line 154, in _read_chr_split_files
out = parsefunc(_splitp(chr_arg), _N_CHR, **kwargs)
File "/annotation/ldsc-F/ildsc/ldscore/parse.py", line 103, in ldscore_fromlist
y = ldscore(fh, num)
File "/annotation/ldsc-F/ildsc/ldscore/parse.py", line 147, in ldscore
first_fh = sub_chr(fh, chrs[0]) + suffix
IndexError: list index out of range
Analysis finished at Wed Aug 14 20:19:53 2024 Total time elapsed: 9.15s Traceback (most recent call last): File "ildsc.py", line 651, in
sumstats.estimate_h2(args, log)
File "/annotation/ldsc-F/ildsc/ldscore/sumstats.py", line 329, in estimate_h2
args, log, args.h2)
File "/annotation/ldsc-F/ildsc/ldscore/sumstats.py", line 245, in _read_ld_sumstats
ref_ld = _read_ref_ld(args, log)
File "/annotation/ldsc-F/ildsc/ldscore/sumstats.py", line 82, in _read_ref_ld
'reference panel LD Score', ps.ldscore_fromlist)
File "/annotation/ldsc-F/ildsc/ldscore/sumstats.py", line 154, in _read_chr_split_files
out = parsefunc(_splitp(chr_arg), _N_CHR, **kwargs)
File "/annotation/ldsc-F/ildsc/ldscore/parse.py", line 103, in ldscore_fromlist
y = ldscore(fh, num)
File "/annotation/ldsc-F/ildsc/ldscore/parse.py", line 147, in ldscore
first_fh = sub_chr(fh, chrs[0]) + suffix
IndexError: list index out of range