finemap

craft.finemap.finemap(data_dfs, index_df, file_dir, n_causal_snps)[source]

Runs Finemap and LDStore on each SNP locus.

Finemap(v1.3.1) was created by Christian Brenner (http://www.christianbenner.com/) and uses summary statistics for finemapping.

INPUT 1. Master file

2. Z file (dataset, uncompressed) The dataset.z file is a space-delimited text file and contains the GWAS summary statistics one SNP per line. It contains the mandatory column names in the following order.

rsid contains the SNP identifiers. The identifier can be a rsID number or a combination of chromosome name and genomic position (e.g. XXX:yyy)

chromosome contains the chromosome names. The chromosome names can be chosen freely with precomputed SNP correlations (e.g. ‘X’, ‘0X’ or ‘chrX’)

position contains the base pair position for each SNP

allele1 contains the “first” allele of the SNPs. In SNPTEST this corresponds to ‘allele_A’, whereas BOLT-LMM uses ‘ALLELE1’

allele2 contains the “second” allele of the SNPs. In SNPTEST this corresponds to ‘allele_B’, whereas BOLT-LMM uses ‘ALLELE0’

maf contains the minor allele frequencies

beta contains the estimated effect sizes as given by GWAS software

se contains the standard errors of effect sizes as given by GWAS software

  1. LD file
    Generated using LDstore, assuming PLINK input files (.bed, .bim, .fam).

Other input options (support for BGEN input data, optional K file) are described at Christian Brenner’s website and are not used here.

OUTPUT