Difference between revisions of "Polymutt2"
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== Download == | == Download == | ||
*The latest version of source code v0.1 can be [[Media:Polymutt2.0.1.tar.gz | downloaded]] here. | *The latest version of source code v0.1 can be [[Media:Polymutt2.0.1.tar.gz | downloaded]] here. | ||
− | *The genetic map files can be [[Media:genetic_map_HapMapII_GRCh37.tar.gz | downloaded]] here. | + | *The genetic map files (genetic_map_GRCh37_chr1.txt) used above can be [[Media:genetic_map_HapMapII_GRCh37.tar.gz | downloaded]] here. |
− | *The clean and common variants in the 1000 Genome Project (1000G.SNV.clean.MAF0.05.tbl.gz) can be [[Media:1000G.SNV.clean.MAF0.05.tbl.gz | downloaded]] here. | + | *The clean and common variants in the 1000 Genome Project (1000G.SNV.clean.MAF0.05.tbl.gz) used above can be [[Media:1000G.SNV.clean.MAF0.05.tbl.gz | downloaded]] here. |
Revision as of 23:08, 1 July 2015
Updates
The latest version of 0.1 is available for 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 and a map file as input
Usage
- NOTE: current version can only process one chromosome at a time
- 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 --max_r2 0.2 --min_avg_dp 2 --out_map chr1.r0.2.map
- 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 --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
- The latest version of source code v0.1 can be downloaded here.
- The genetic map files (genetic_map_GRCh37_chr1.txt) used above can be downloaded here.
- The clean and common variants in the 1000 Genome Project (1000G.SNV.clean.MAF0.05.tbl.gz) used above can be downloaded here.