Variant classification
From Genome Analysis Wiki
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 loosely defined 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.
- 4. CLUMPED
- a. A clumping of nearby SNPs, MNPs or Indels.
- 5. SV
- The alternate sequence is represented by a angled bracket tag.
Classification Procedure
- 1. Trim each allele
- 2. Inspect length to define INDEL and count insertions or deletions
- 3. Inspect overlapping fragments to count transitions and transversions
- a. if shorter allele is of length 1, check overlap on both ends,
- if one of the ends match, ignore ts/tv counts.
- else, align strictly on 5' end and count transitions and transversions.
- b. If all overlapping nucleotides do not match, assign SNP if shorter allele is of length 1 and MNP if not.
- 4. If all alleles are the same length, assign MNP to the entire variant.
Examples
We present the following examples to explain the concepts explained earlier.
Legend for examples
<variant classification>
REF <reference sequence> ALT <alternative sequence 1> #<allele classification>, <contribution to transition, transversion, insertion or deletion count> ALT <alternative sequence 2> #<allele classification>, <contribution to transition, transversion, insertion or deletion count>
Simple Biallelic Examples
SNP
REF A ALT G #SNP, 1 ts
MNP
REF AT ALT GC #MPN, 2 ts
INDEL
REF AT ALT A #INDEL, 1 del
INDEL
REF AT ALT T #INDEL, 1 del
SV
REF A ALT <DEL> #SV
Complex Biallelic Examples
SNP|INDEL
REF AT ALT G #SNP, INDEL, 1 ts
MNP|INDEL
REF ATT ALT GG #MNP, INDEL, 1 ts, 1 tv, 1 del
MNP|CLUMPED
REF ATTTT ALT GTTTC #MNP, CLUMEPD, 2 ts #since all the alleles are of the sample length, classified as MNP too.
INDEL|CLUMPED
REF ATTTTTTTT ALT GTTTC #INDEL, CLUMPED, 2 ts, 1 del
Simple Multiallelic Examples
SNP
REF A ALT G #SNP, 1 ts ALT C #SNP, 1 tv
MNP
REF AG ALT GC #MNP, 1 ts, 1 tv ALT CT #MNP, 2 tv
INDEL
REF ATTT ALT ATT #INDEL, 1 del ALT ATTTT #INDEL, 1 ins
Complex Multiallelic Examples
SNP|MNP
REF AT ALT GT #SNP, 1 ts ALT AC #SNP, 1 ts #since all the alleles are of the sample length, classified as MNP too.
SNP|MNP|CLUMPED
REF ATTTG ALT GTTTC #CLUMPED, 1 ts, 1 tv ALT ATTTC #SNP, 1 tv #since all the alleles are of the sample length, classified as MNP too.
SNP|MNP|INDEL
REF GT ALT CT #SNP, 1 tv ALT AG #MNP, 2 tv ALT GTT #INDEL, 1 ins
SNP|MNP|INDEL|CLUMPED
REF GTTT ALT CG #MNP, INDEL, 2 tv, 1 del ALT AG #MNP, INDEL, 1 ts, 1 tv ALT GTGTG #SNP, INDEL, CLUMPED, 1 tv, 1 ins
Weird Examples
Structured Variants Examples
no. of structural variants : 41217
2 alleles : 38079
deletion : 13135 <DEL>
insertion : 16451 <INS>
mobile element : 16253 <INS:ME>
ALU : 12513 <INS:ME:ALU>
LINE1 : 2911 <INS:ME:LINE1>
SVA : 829 <INS:ME:SVA>
numt : 198 <INS:MT>
duplication : 664 <DUP>
inversion : 100 <INV>
copy number variation : 7729 <CN4>
>=3 alleles : 3138
copy number variation : 3138 <CN4>,<CN8>
Output
This is the annotated output of peek in the vt suite.
stats:no. of samples : 0 #number of genotype fields in VCF file, this is a site list so it is 0
no. of chromosomes : 25 #no. of chromosomes observed in this file.
========== Micro variants ==========
no. of SNP : 54247827 #total number of SNPs
2 alleles : 53487808 (1.99) [35616038/17871770] #ts/tv ratio and the respective counts
3 alleles : 389190 (0.60) [291224/487156]
4 alleles : 370828 (0.50) [370828/741656]
>=5 alleles : 1 (0.33) [1/3]
no. of MNP : 122125
2 alleles : 121849 (1.56) [152383/97816]
3 alleles : 273 (0.89) [537/601]
4 alleles : 3 (1.00) [9/9]
no. of Indel : 6600770
2 alleles : 6285861 (0.88) [2937096/3348765] #ins/del ratio and the respective counts
3 alleles : 280892 (8.72) [503977/57807]
4 alleles : 28245 (131.19) [84094/641]
>=5 alleles : 5772 (3847.00) [23082/6]
no. of SNP/MNP : 1161
3 alleles : 1143 (1.57) [1565/994]
4 alleles : 15 (1.36) [34/25]
>=5 alleles : 3 (0.67) [8/12]
no. of SNP/Indel : 115153
2 alleles : 42717 (0.65) [16778/25939] (0.57) [15441/27276] #ts/tv and ins/del ratios
3 alleles : 66401 (0.72) [29681/41397] (0.33) [31458/96168]
4 alleles : 4631 (0.55) [2420/4386] (0.25) [2602/10306]
>=5 alleles : 1404 (0.62) [1197/1926] (0.10) [513/4989]
no. of MNP/Indel : 15619
2 alleles : 12820 (0.51) [12099/23648] (0.77) [5594/7226]
3 alleles : 2455 (0.40) [1796/4469] (0.45) [1144/2546]
4 alleles : 292 (0.24) [215/891] (1.42) [415/292]
>=5 alleles : 52 (0.43) [96/225] (2.47) [126/51]
no. of SNP/MNP/Indel : 273
3 alleles : 167 (0.63) [201/321] (0.38) [70/184]
4 alleles : 85 (0.35) [71/203] (0.28) [31/111]
>=5 alleles : 21 (0.35) [24/68] (0.68) [25/37]
no. of MNP/Clumped : 61175
2 alleles : 60617 (1.68) [84410/50220]
3 alleles : 549 (1.23) [1777/1449]
4 alleles : 8 (1.43) [53/37]
>=5 alleles : 1 (1.00) [5/5]
no. of SNP/MNP/Clumped : 290
3 alleles : 282 (1.35) [665/494]
4 alleles : 8 (0.57) [13/23]
no. of Indel/Clumped : 27638
2 alleles : 25971 (0.65) [31435/48526] (0.79) [11444/14527]
3 alleles : 1585 (0.74) [3568/4793] (0.87) [1383/1582]
4 alleles : 70 (0.55) [96/175] (1.61) [124/77]
>=5 alleles : 12 (0.59) [37/63] (4.71) [33/7]
no. of SNP/Indel/Clumped : 456
3 alleles : 257 (0.84) [332/394] (0.33) [111/340]
4 alleles : 174 (0.38) [105/279] (0.58) [186/321]
>=5 alleles : 25 (0.19) [12/63] (0.94) [44/47]
no. of MNP/Indel/Clumped : 153
3 alleles : 138 (0.50) [233/466] (0.84) [102/122]
4 alleles : 12 (0.35) [14/40] (1.42) [17/12]
>=5 alleles : 3 (0.64) [7/11] (0.67) [4/6]
no. of SNP/MNP/Indel/Clumped : 6
4 alleles : 1 (3.00) [3/1] (0.00) [0/3]
>=5 alleles : 5 (0.62) [8/13] (2.00) [12/6]
no. of Reference : 0
====== Other useful categories =====
no. of Block Substitutions : 184751 #equivalent to categories with allele lengths that are the same.
2 alleles : 182466 (1.60) [236793/148036]
3 alleles : 2247 (1.28) [4544/3538]
4 alleles : 34 (1.16) [109/94]
>=5 alleles : 4 (0.76) [13/17]
no. of Complex Substitutions : 159298 #equivalent to categories not including simple SNPs, Block Substitutions and Simple Indels
2 alleles : 81508 (0.61) [60312/98113] (0.66) [32479/49029]
3 alleles : 71003 (0.69) [35811/51840] (0.34) [34268/100942]
4 alleles : 5265 (0.49) [2924/5975] (0.30) [3375/11122]
>=5 alleles : 1522 (0.58) [1381/2369] (0.15) [757/5143]
======= 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 observed variants : 79449759
no. of unclassified variants : 0
Implementation
This is implemented in vt.
Maintained by
This page is maintained by Adrian.
