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→Configuration File
In the config file, there are several parameters to adjust:
In the config file, there are several parameters to adjust:
INDEX_SNP_FILE: This file lists the trait-associated input SNPs. In this file, there is a single column without a header. Index SNPs can be in rsid or chr:pos format.
INDEX_SNP_FILE: This file lists the trait-associated input SNPs. In this file, there is a single column without a header. Index SNPs can be in rsid or hg19 chr:pos format.
BED_FILE_INDEX: This file lists the BED files to be used for enrichment analysis. Use complete paths to their locations.
BED_FILE_INDEX: This file lists the datasets (e.g. BED files) to be used for enrichment analysis. Use complete paths to file locations and make sure positions are in hg19 format.
R2THRESHOLD and LDWINDOWSIZE: These two parameters define the index SNP LD proxies by R2 threshold and LD window size.
R2THRESHOLD and LDWINDOWSIZE: These two parameters define the index SNP LD proxies by R2 threshold and LD window size.
