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, 18:52, 10 April 2014
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| == Updates == | | == Updates == |
| The latest version of 0.1 is available for [[#Download | Download]]. | | The latest version of 0.1 is available for [[#Download | Download]]. |
| + | |
| + | == Compilation == |
| + | *After downloading the source code, unzip and untar it, and cd polymutt2, and then type Make |
| + | *Two executables will be generated in bin/ directory: polymutt2 and vcf2map |
| + | * vcf2map is to prune LD and generate a map file with high quality SNPs |
| + | * polymutt2 is to generate genotype calls taking a VCF file as input |
| + | |
| + | == Usage == |
| + | * vcf2map |
| + | 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 |
| + | |
| + | * polymutt2 |
| + | 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 --fam_id fam1 |
| + | polymutt2 -p input.ped -m chr1.map --in_vcf input.vcf --out_vcf out.vcf --out_range 1:1000000-2000000 |
| | | |
| == Download == | | == Download == |