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, 10:12, 27 April 2014
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| + | == NOTE == |
| + | If you are interested in calling '''''de novo''''' mutations in '''trios''' based on '''VCF''' files, we recommend our new tool, triodenovo, which implemented a nicer algorithm with a more natural interpretation of the ''''''de novo''''' quality. Please check it out following the link below. Thanks for trying it out! |
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| + | http://genome.sph.umich.edu/wiki/Triodenovo |
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| == Updates == | | == Updates == |
− | The latest version of 0.16 is available for [[#Download | Download]]. | + | The latest version of 0.18 is available for [[#Download | Download]]. |
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| + | v0.18 fixed a bug when it reported inbreeding for some pedigrees which are not inbreeding families |
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| + | v0.17 fixed a bug when some of the samples in the per files are not in the input vcf file |
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| v0.16 fixed a bug when the input is a VCF file with multiple nuclear families and the ped file contains only a single nuclear family. | | v0.16 fixed a bug when the input is a VCF file with multiple nuclear families and the ped file contains only a single nuclear family. |
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| polymutt -p input.ped -d input.dat --in_vcf input.vcf --out_vcf out.vcf --nthreads 4 | | polymutt -p input.ped -d input.dat --in_vcf input.vcf --out_vcf out.vcf --nthreads 4 |
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− | Examples for ''de novo'' mutation detection (works only for GLF files): | + | Examples for ''de novo'' mutation detection |
| polymutt -p input.ped -d input.dat -g input.gif --denovo --out_vcf out.denovo.vcf --nthreads 4 | | polymutt -p input.ped -d input.dat -g input.gif --denovo --out_vcf out.denovo.vcf --nthreads 4 |
− | polymutt -p input.ped -d input.dat -g input.gif --denovo --rate_denovo 1.2e-06 --out_vcf out.denovo.vcf --nthreads 4 | + | polymutt -p input.ped -d input.dat -g input.gif --out_vcf out.vcf --denovo |
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| Examples of calling X, Y and MT (works only for variants but not de novo mutations): | | Examples of calling X, Y and MT (works only for variants but not de novo mutations): |
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| == Download == | | == Download == |
− | The latest version of source code v0.15 with test files can be [[Media:Polymutt.0.15.tar.gz | downloaded]] here. | + | The latest version of source code v0.18 with test files can be [[Media:Polymutt.0.18.tar.gz | downloaded]] here. |
− | A precompiled version of 0.14 on Ubuntu 10.04 (works on CentOS 6.3 as well) is available for [[Media:polymutt.0.14.precompiled.tar.gz | download]]
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| == Contact == | | == Contact == |