Variant classification

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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.

On this wiki page, we describe a a variant classification system for VCF variants.

Definitions

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.

Example

Summarizes the variants in a VCF file

  #summarizes the variants found in mills.vcf
  vt peek mills.vcf
 usage : vt peek [options] <in.vcf>
 options : -o  output VCF file [-]
           -I  file containing list of intervals []
           -i  intervals []
           -r  reference sequence fasta file []
           --  ignores the rest of the labeled arguments following this flag
           -h  displays help
#This is a sample output of a peek command which summarizes the variants found in a VCF file.
  stats: no. of samples                     :          0
         no. of chromosomes                 :         22
========== Micro variants ==========
no. of SNPs  : 77228885 2 alleles (ts/tv)  : 77011302 (2.11) [52287790/24723512] 3 alleles (ts/tv)  : 216560 (0.75) [185520/247600] 4 alleles (ts/tv)  : 1023 (0.50) [1023/2046]
no. of MNPs  : 0 2 alleles (ts/tv)  : 0 (-nan) [0/0] >=3 alleles (ts/tv)  : 0 (-nan) [0/0]
no. Indels  : 2147564 2 alleles (ins/del)  : 2124842 (0.47) [683250/1441592] >=3 alleles (ins/del)  : 22722 (2.12) [32411/15286]
no. SNP/MNP  : 0 3 alleles (ts/tv)  : 0 (-nan) [0/0] >=4 alleles (ts/tv)  : 0 (-nan) [0/0]
no. SNP/Indels  : 12913 2 alleles (ts/tv) (ins/del)  : 412 (0.41) [120/292] (3.68) [324/88] >=3 alleles (ts/tv) (ins/del)  : 12501 (0.43) [7670/17649] (18.64) [12434/667]
no. MNP/Indels  : 153 2 alleles (ts/tv) (ins/del)  : 0 (-nan) [0/0] (-nan) [0/0] >=3 alleles (ts/tv) (ins/del)  : 153 (0.30) [138/465] (0.27) [67/248]
no. SNP/MNP/Indels  : 2 3 alleles (ts/tv) (ins/del)  : 0 (-nan) [0/0] (-nan) [0/0] 4 alleles (ts/tv) (ins/del)  : 2 (0.00) [3/5] (1.00) [3/3] >=5 alleles (ts/tv) (ins/del)  : 0 (-nan) [0/0] (-nan) [0/0]
no. of clumped variants  : 19025 2 alleles  : 0 (-nan) [0/0] (-nan) [0/0] 3 alleles  : 18508 (0.16) [12152/75366] (0.00) [93/18653] 4 alleles  : 451 (0.15) [369/2390] (0.33) [201/609] >=5 alleles  : 66 (0.09) [37/414] (1.19) [107/90]
====== Other useful categories =====
no. complex variants  : 32093 2 alleles (ts/tv) (ins/del)  : 412 (0.41) [120/292] (3.68) [324/88] >=3 alleles (ts/tv) (ins/del)  : 31681 (0.21) [20369/96289] (0.64) [12905/20270]
======= Structural variants ========
no. of structural variants  : 41217 2 alleles  : 38079 deletion  : 13135 insertion  : 16451 mobile element  : 16253 ALU  : 12513 LINE1  : 2911 SVA  : 829 numt  : 198 duplication  : 664 inversion  : 100 copy number variation  : 7729 >=3 alleles  : 3138 copy number variation  : 3138
========= General summary ==========
no. of reference  : 0
no. of observed variants  : 79449759 no. of unclassified variants  : 0

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This page is maintained by Adrian.