Difference between revisions of "Polymutt2"
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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 == |
Revision as of 18:52, 10 April 2014
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 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
- The latest version of source code v0.1 can be downloaded here.
- The genetic map files can be downloaded here.
- The clean and common variants in the 1000 Genome Project can be downloaded here.