Pipeline for GWAS simulation and formatting for multiple analysis methods
Full Disease Gene Mapping Pipeline
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Simupop simulation using human genome as starting point. a. initial population from Hapmap data loadHapMap3.py selectMarkers.py -select hapmap populations -select chromosomes (by name) -select markers (number of markers + start, range, list of SNPs) b. expand population under selection -names of markers under selection -selection regime c. generate case/control datasets using a penetrance model -penetrance.py single gene alleles additive or multiplicative? multiple Gene genes and alleles additive/multiplicative? wild type risk? relative risk? number of cases number of controls d. remove monomorphic markers (and DPL?) from datasets remove_rare_snps.py remove_DPL.py
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Generation of input datafiles for various disease mapping programs. a. simupop_formatr.py - names of programs b. marg_split.py (makes sliding windows)
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Generation of script files for running programs on SGE cluster. a. program-specific options (number of ARGs, number of permutations, etc) b. SGE options (memory, number of machines) c. is it to be run as an "array"? program-specific array intstructions
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Generation of script files for collecting results. a. based on the programs run: need to stitch windows back together?
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Generation of pipeline-run INSTRUCTIONS.