“Variant Normalization”的版本间的差异
（创建页面，内容为“== Introduction == The Variant Call Format (VCF) is a flexible file format specification that allows us to represent many different variant types ranging from SNPs,…”） |
Suqingdong（讨论 | 贡献） |
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| + | __TOC__ | ||
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== Introduction == | == 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. | 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. | 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}} | ||
| + | |||
| + | <comments /> | ||
2020年1月18日 (六) 09:39的最新版本
目录
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:
A variant is parsimonious if and only if it is represented in as few nucleotides as possible an allele of length 0.
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
测试
hello world
图片引用
参考
| 用户留言： |
为什么要对VCF进行norm操作？norm是针对INDEL不同表示形式的统一 |
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