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Variant Normalization
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__TOC__ == Introduction == The Variant Call Format (VCF) is a flexible file format specification that allows us to represent many different variant types ranging from SNPs, indels to copy number variations. However, variant representation in VCF is non-unique for variants that have explicitly expressed reference and alternate sequences. A failure to recognize this will frequently result in inaccurate analyses. On this wiki page, we describe a variant normalization procedure that is well defined for biallelic as well as multiallelic variants. We then provide a formal proof the procedure's correctness. == Definition == The normalization of a variant representation in VCF consists of two parts: parsimony and left alignment pertaining to the nature of a variant's length and position respectively. ==== Parsimony ==== In the context of variant representation, parsimony means representing a variant in as few nucleotides as possible without reducing the length of any allele to 0. It is a property describing the nature of the length of a variant's alleles and is defined as follows: <pre> A variant is parsimonious if and only if it is represented in as few nucleotides as possible an allele of length 0. </pre> == 测试边框 == * solid 单线边框 ** border:1px solid #808080 常用边框之一,推荐 * dashed 虚线边框 ** border:1px dashed #808080 常用边框之一,推荐 * double 双线边框 ** border:3px double #808080 常用双线边框之一,推荐 <div style="width:100px; color:yellow; background:#FF0000;border:5px double #FFFFFF;"> 测试 </div> <h1>hello world</h1> == 图片引用 == [[文件:PAH.png]] == 参考 == * https://www.liwei8090.com/10586.html * https://genome.sph.umich.edu/wiki/Variant_Normalization [[category:常见问题]] ---- {{SQD的模板}}
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