Changes

From Genome Analysis Wiki
Jump to: navigation, search

Variant classification

4,628 bytes added, 09:13, 5 September 2014
Definitions
= 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
 
<div class=" mw-collapsible mw-collapsed">
#summarizes the variants found in mills.vcf
vt peek mills.vcf
 
<div class="mw-collapsible-content">
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
</div>
</div>
 
#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<br>
========== Micro variants ==========<br>
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]<br>
no. of MNPs : 0
2 alleles (ts/tv) : 0 (-nan) [0/0]
>=3 alleles (ts/tv) : 0 (-nan) [0/0]<br>
no. Indels : 2147564
2 alleles (ins/del) : 2124842 (0.47) [683250/1441592]
>=3 alleles (ins/del) : 22722 (2.12) [32411/15286]<br>
no. SNP/MNP : 0
3 alleles (ts/tv) : 0 (-nan) [0/0]
>=4 alleles (ts/tv) : 0 (-nan) [0/0] <br>
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]<br>
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]<br>
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]<br>
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]<br>
====== Other useful categories =====<br>
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]<br>
======= Structural variants ========<br>
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 <br>
========= General summary ========== <br>
no. of reference : 0 <br>
no. of observed variants : 79449759
no. of unclassified variants : 0
= Maintained by =
This page is maintained by [mailto:atks@umich.edu Adrian].
1,102
edits

Navigation menu