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* NOTE: current version can only process one chromosome at a time
* NOTE: current version can only process one chromosome at a time
== Examples of generating the map file ==
* vcf2map: generate a sparse map file (see [[#Download|Download]] for files genetic_map_GRCh37_chr1.txt and 1000G.SNV.clean.MAF0.05.tbl.gz)
* vcf2map: generate a sparse map file (see [[#Download|Download]] for files genetic_map_GRCh37_chr1.txt and 1000G.SNV.clean.MAF0.05.tbl.gz)
vcf2map --vcf input.vcf --ped input.ped --map genetic_map_GRCh37_chr1.txt --include_list 1000G.SNV.clean.MAF0.05.tbl.gz --out_map chr1.map
vcf2map --vcf input.vcf --ped input.ped --map genetic_map_GRCh37_chr1.txt --include_list 1000G.SNV.clean.MAF0.05.tbl.gz --out_map chr1.map
* User defined r2 cutoff for LD pruning , min of average depth for filtering
vcf2map --vcf input.vcf --ped input.ped --map genetic_map_GRCh37_chr1.txt --include_list 1000G.SNV.clean.MAF0.05.tbl.gz --max_r2 0.2 --min_avg_dp 2 --out_map chr1.r0.2.map
== Examples of running polymutt2 ==
* polymutt2: taking a VCF and the map file generated by vcf2map (the vcf file can be a complete vcf with all variants and samples)
* polymutt2: taking a VCF and the map file generated by vcf2map (the vcf file can be a complete vcf with all variants and samples)
