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, 23:54, 10 November 2016
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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]]. |
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| + | == Note == |
| + | '''Polymutt2 can only handle one chromosome, so please run it chromosome by chromosome'''. |
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| == Compilation == | | == Compilation == |
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| * 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 |
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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 v0.2 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. |
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| == Contact == | | == Contact == |
− | For questions please contact the authors (Bingshan Li: [mailto:bingshan@umich.edu bingshan@umich.edu]) | + | For questions please contact the authors (Bingshan Li: [mailto:bingshan.li@vanderbilt.edu bingshan.li@vanderbilt.edu]) |
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| == Citation == | | == Citation == |
| Li B, Wei Q, Zhan X, Zhong X, Chen W, Li C, et al. (2015) Leveraging Identity-by-Descent for Accurate Genotype Inference in Family Sequencing Data. PLoS Genet 11(6): e1005271. doi:10.1371/journal.pgen.1005271 | | Li B, Wei Q, Zhan X, Zhong X, Chen W, Li C, et al. (2015) Leveraging Identity-by-Descent for Accurate Genotype Inference in Family Sequencing Data. PLoS Genet 11(6): e1005271. doi:10.1371/journal.pgen.1005271 |