Variant classification

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 definition of a variant is based on the definition of each allele with respect to the reference sequence. We consider 5 major types as follows.

1. SNP

The reference and alternate sequences are of length 1 and the base nucleotide is different from one another.

2. MNP

a.The reference and alternate sequences are of the same length and have to be greater than 1 and all nucleotides in the sequences differ from one another.

OR

b. all reference and alternate sequences have the same length.

3. INDEL

a. The reference and alternate sequence are not the same length.

AND

b. The removal of a subsequence of the longer sequence would reduce the longer sequence to the smaller sequence.

4. CLUMPED

5. SV

The alternate sequence is represented by a angled bracket tag - , for example.

Simple Examples

   SNP

   REF  A    
   ALT  G

   MNP

   REF  AT    
   ALT  GC

   INDEL

   REF  AT    
   ALT  A

   SV

   REF  A    
   ALT  

Complex Examples

   SNP

   REF  A    
   ALT  G

   MNP

   REF  AT    
   ALT  GC

Output

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

Maintained by

This page is maintained by Adrian.