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In the configure file, there are 8 parameters to adjust:
In the configure file, there are 8 parameters to adjust:
INDEX_SNP_FILE: This file lists the trait-associated input SNPs for enrichment analysis. 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 chr:pos format.
BED_FILE_INDEX: This is a file listing the BED files with complete paths to their locations to be used for enrichment analysis.
BED_FILE_INDEX: This file lists the BED files to be used for enrichment analysis. Use complete paths to their locations.
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.
== Acknowledgements ==
== Acknowledgements ==
FallInBed is a result from collaborative efforts by Cristen Willer, Jin Chen, Wei Zhou, Ellen Schmidt, He Zhang, and Goncalo Abecasis. Please email Cristen Willer [cristen@umich.edu] for any questions.
FallInBed is the result of collaborative efforts by Cristen Willer, Jin Chen, Wei Zhou, Ellen Schmidt, He Zhang, and Goncalo Abecasis. Please email Cristen Willer [cristen@umich.edu] for any questions.
