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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
* vcf2map
* vcf2map: generate a sparse map file
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
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
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
* polymutt2
* polymutt2: taking a VCF and the map file generated by vcf2map
polymutt2 -p input.ped -m chr1.map --in_vcf input.vcf --out_vcf out.vcf
polymutt2 -p input.ped -m chr1.map --in_vcf input.vcf --out_vcf out.vcf
polymutt2 -p input.ped -m chr1.map --in_vcf input.vcf --out_vcf out.vcf --best_path
polymutt2 -p input.ped -m chr1.map --in_vcf input.vcf --out_vcf out.vcf --best_path
