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== Updates ==
== Updates ==
The latest version of 0.1 is available for [[#Download | Download]].
The latest version of v0.2 is available for [[#Download | Download]].
== Note ==
'''Polymutt2 can only handle one chromosome, so please run it chromosome by chromosome'''.
== Compilation ==
== Compilation ==
* If only a range is desire to output (for example the whole chromosome can be divided into multiple parallel jobs each working on a range)
* If only a range is desire to output (for example the whole chromosome can be divided into multiple parallel jobs each working on a range)
polymutt2 -p input.ped -m chr1.map --in_vcf input.vcf --out_vcf out.vcf --out_range 1:1000000-2000000
polymutt2 -p input.ped -m chr1.map --in_vcf input.vcf --out_vcf out.vcf --out_range 1:1000000-2000000
== File format ==
See PLINK http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml for file format
== 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 v0.2 can be [[Media:Polymutt2_v0.2.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 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) used above 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.
