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, 16:07, 4 December 2013
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| ''NOTE'': <code>--annoType Nonsynonymous</code> will only analyze nonsynonymous variants where they have <code>ANNO=Nonsynonymous</code> in the INFO field. VCF with annotatino information are called annotated VCF here. And to annotate a VCF file, you can use [https://github.com/zhanxw/anno ANNO], a fast and accurate annotation software. | | ''NOTE'': <code>--annoType Nonsynonymous</code> will only analyze nonsynonymous variants where they have <code>ANNO=Nonsynonymous</code> in the INFO field. VCF with annotatino information are called annotated VCF here. And to annotate a VCF file, you can use [https://github.com/zhanxw/anno ANNO], a fast and accurate annotation software. |
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− | == Genotyep filters == | + | == Genotype filters == |
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| Genotype with low depth or low quality can be filtered out by these options: | | Genotype with low depth or low quality can be filtered out by these options: |