LD matrix generation

Note

Snps in the fine-mapping file should be in the same order as in the LD matrix file

LD matrix generation using PAINTOR script

Header Option Note
chr required Used to choose the reference file
pos required
effective allele required
baseline allele required
Zscore required
1000g reference required
1000g panel file required
population ethnicity required

Usually 1000 genome reference file are splitted into chromosomes, and CalcLD_1KG_VCF.py need to specify reference with matched chromosome

Example code

Note

This should not be used directly since it applies to specific files

    python CalcLD_1KG_VCF.py
    --locus gwas_summary_3_4750808.processed
    --reference ALL.chr3.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
    --map integrated_call_samples_v3.20130502.ALL.panel
    --effect_allele effect_allele
    --alt_allele baseline_allele
    --population EAS
    --Zhead Zscore
    --out_name gwas_summary_3_4750808.processed
    --position pos

to be added