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kkdey / GSSG

Gene Set + S2G strategy annotations analyzed for disease architecture
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LD Scores for concatenation must have identical SNP columns. #30

Open C0nc opened 8 months ago

C0nc commented 8 months ago

Sorry, but the snp number in the baselineLD_v2.1_annots download from the Google Cloud can not match the one generated by the user.

ValueError: LD Scores for concatenation must have identical SNP columns.

and I encountered this problem when following the command the reproduce the article results in the final run_ldsc_reg.sh process

SidSouthekal-Lilly commented 3 months ago

@C0nc I am getting the same error, were you able to resolve it? Also tried switching to previous ldsc commit and different baseline version files.

Call: ./ldsc.py \ --h2 SUMSTATS_PATH/UKB_460K.biochemistry_Glucose.sumstats \ --ref-ld-chr sclinker_Annots/sclinker_DiseaseProgram /Disease_Innate.lymphoid.cell/ABC_Road_FAT/ABC_Road_FAT.,LDSC_PATH/baselineLD_v2.1_annots/baselineLD. \ --out sclinker_out/baselineLD_v2.1_annots/sclinker_DiseaseProgram /Disease_Innate.lymphoid.cell/ABC_Road_FAT/UKB_460K.biochemistry_Glucose.sumstats \ --overlap-annot \ --frqfile-chr LDSC_PATH/1000G_Phase3_frq/1000G.EUR.QC. \ --w-ld-chr LDSC_PATH/weights_hm3_no_hla. \ --print-coefficients \ --print-delete-vals

Beginning analysis at Mon Mar 11 11:27:57 2024 Reading summary statistics from SUMSTATS_PATH/UKB_460K.biochemistry_Glucose.sumstats ... Read summary statistics for 1187344 SNPs. Reading reference panel LD Score from sclinker_Annots/sclinker_DiseaseProgram/Disease_Innate.lymphoid.cell/ABC_Road_FAT/ABC_Road_FAT.,LDSC_PATH/baselineLD_v2.1_annots/baselineLD.[1-22] ... Error parsing reference panel LD Score. Traceback (most recent call last): File " /ldsc/ldsc.py", line 644, in sumstats.estimate_h2(args, log) File " /ldsc/ldscore/sumstats.py", line 326, in estimate_h2 args, log, args.h2) File "/ldsc/ldscore/sumstats.py", line 243, in _read_ld_sumstats ref_ld = _read_ref_ld(args, log) File "/ldsc/ldscore/sumstats.py", line 82, in _read_ref_ld 'reference panel LD Score', ps.ldscore_fromlist) File "/ldsc/ldscore/sumstats.py", line 155, in _read_chr_split_files raise e ValueError: LD Scores for concatenation must have identical SNP columns.