bulik / ldsc

LD Score Regression (LDSC)
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Error calculating heritability #389

Open DelnazRoshandel opened 1 year ago

DelnazRoshandel commented 1 year ago

I am trying to calculate heritability and getting this error:

Reading regression weight LD Score from baselineLD_v2.3/baselineLD.[1-22] ... (ldscore_fromlist) Traceback (most recent call last): File "/hpf/tools/centos7/ldsc/1.0.1/ldsc.py", line 644, in sumstats.estimate_h2(args, log) File "/hpf/tools/centos7/ldsc/1.0.1/ldscore/sumstats.py", line 326, in estimate_h2 args, log, args.h2) File "/hpf/tools/centos7/ldsc/1.0.1/ldscore/sumstats.py", line 247, in _read_ld_sumstats w_ld = _read_w_ld(args, log) File "/hpf/tools/centos7/ldsc/1.0.1/ldscore/sumstats.py", line 136, in _read_w_ld raise ValueError('--w-ld may only have one LD Score column.') ValueError: --w-ld may only have one LD Score column.

I am wondering what causing the problem.

aksarkar commented 1 year ago

The files baselineLD_v2.3/* are not appropriate to use as regression weights in --w_ld.

You need to use the files in 1000G_Phase3_weights_hm3_no_MHC.tgz (https://zenodo.org/record/7768714) for example.