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Example for LDSPEC CLI

Toy pipeline showcasing steps for running LDSPEC.

LDSPEC CLI flags

  • --job: one of get_snp_block, compute_ld, compute_score, compute_avgr, regress.
  • --pgen_file: prefix of PLINK2 pgen files. @ refers to CHR number.
  • --ld_file: LDSPEC LD files.
  • --annot_file: LDSPEC annotation files.
  • --score_file: LDSPEC LD score files.
  • --snp_range_file: LDSPEC SNP range file.
  • --sumstats_file: Summary statistics files, same as in LDSC.
  • --avgr_file: LDSPEC .avgr file for average r in SNP-pair annotations.
  • --prefix_out: Output prefix.
  • --snp_range: SNP range, e.g., --snp_range c1_s0_e10000 for the first 10,000 SNPs on chromosome 1.
  • --win_size: window size, e.g., --win_size 1e7 for a 10Mb LD window.
  • --flag_nofil_snp: If to filter SNPs in regression, default --flag_nofil_snp False.

Step 1: get SNP blocks

Create .snp_range.txt file with SNP ranges. Example: ldspec_s1.snp_range.txt.

job=get_snp_block: generate SNP blocks (10,000 SNPs per block)
- Input : --job | --pgen_file | --prefix_out
- Output : list of snp ranges (in the format of "snp_range"), e.g., `c1_s0_e10000`.

Step 2: compute LD matrices

Compute LD matrix for each SNP block in the .snp_range.txt file; can parallelize.

job=compute_ld : compute LD between target SNPs in `snp_range` and reference SNPs within `win_size` of target SNPs
- Input : --job | --pgen_file | --prefix_out | --snp_range | [--win_size]
- Output : `_ld.npz` file; LD matrix.

Step 3: compute LD score

Compute LD score for each SNP block in the snp_range.txt file; can parallelize.

--annot_file takes comma seperated .annot.gz and .pannot_mat.npz files, or a .txt file of file paths.

compute_score : compute LD and DLD scores.
- Input : --job | --pgen_file | --ld_file | --annot_file | --prefix_out | [--win_size] | [--flag_cross_term]
- Output : `_score.tsv.gz` file; LD and DLD scores.

Step 4: combine LD scores

--score_file: @ represents snp_range

combine_score : concatenate scores from the same CHR 
- Input : --score_file | --snp_range_file | --prefix_out
- Output : concatenated score files by CHR

Step 5: compute AVGR

Compute average LD (avgr) for each pannot.

compute_avgr : compute average LD (avgr) for each pannot. "--ld_file" should contain all LD files
- Input : --job | --pgen_file | --ld_file | --annot_file | --prefix_out
- Output : Average LD for each pannot.

Step 6: regress

Estimate LDSPEC results. --avgr_file supports comma-separated .avgr files.

regress : estimate LDSPEC parameters.
- Input : --job | --pgen_file | --annot_file  | --score_file | --sumstats_file| --avgr_file | --prefix_out | [--flag_cross_term] | [--flag_nofil_snp]
- Output : LD-SPEC result.