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, 23:30, 1 July 2015
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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 |
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| + | == 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 |
− | 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
| + | |
| + | * 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 == |
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| * 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) |