Step 3: generate_ldscore

usage: gsmap run_generate_ldscore [-h] --workdir WORKDIR --sample_name
                                  SAMPLE_NAME --chrom CHROM --bfile_root
                                  BFILE_ROOT --keep_snp_root KEEP_SNP_ROOT
                                  --gtf_annotation_file GTF_ANNOTATION_FILE
                                  [--gene_window_size GENE_WINDOW_SIZE]
                                  [--enhancer_annotation_file ENHANCER_ANNOTATION_FILE]
                                  [--snp_multiple_enhancer_strategy {max_mkscore,nearest_TSS}]
                                  [--gene_window_enhancer_priority {gene_window_first,enhancer_first,enhancer_only}]
                                  [--spots_per_chunk SPOTS_PER_CHUNK]
                                  [--ld_wind LD_WIND] [--ld_unit {SNP,KB,CM}]
                                  [--additional_baseline_annotation ADDITIONAL_BASELINE_ANNOTATION]

Named Arguments

--workdir

Path to the working directory.

--sample_name

Name of the sample.

--chrom

Chromosome id (1-22) or “all”.

--bfile_root

Root path for genotype plink bfiles (.bim, .bed, .fam).

--keep_snp_root

Root path for SNP files.

--gtf_annotation_file

Path to GTF annotation file.

--gene_window_size

Gene window size in base pairs.

Default: 50000

--enhancer_annotation_file

Path to enhancer annotation file (optional).

--snp_multiple_enhancer_strategy

Possible choices: max_mkscore, nearest_TSS

Strategy for handling multiple enhancers per SNP.

Default: 'max_mkscore'

--gene_window_enhancer_priority

Possible choices: gene_window_first, enhancer_first, enhancer_only

Priority between gene window and enhancer annotations.

--spots_per_chunk

Number of spots per chunk.

Default: 1000

--ld_wind

LD window size.

Default: 1

--ld_unit

Possible choices: SNP, KB, CM

Unit for LD window.

Default: 'CM'

--additional_baseline_annotation

Path of additional baseline annotations