- Created by Jacobo Coll on Oct 04, 2018
You are viewing an old version of this page. View the current version.
Compare with Current View Page History
Version 1 Next »
Overview
A genomic variant is represented by a locus (chromosome + position), reference sequence and list of alternates.
Is common, because of the VCF specification, that the reference and alternate fields contain extra bases not needed for the Variant representation. It is completely valid to specify a variation like chr1:100:AC:AT
, which is absolutely the same variant that chr1:101:C:T
.
The number of possible combinations to represent the same genomic variant is non-unique, so it is mandatory to normalize the representation of the variant in order to determine when two representations are the same or different variants. A failure to recognize this will frequently result in inaccurate analyses.
Steps
The variant normalization focuses on different aspects of the variant representation to make a full normalization.
Chromosome naming
Due to there is not any standard for the chromosome naming, is common to see different names for the same chromosome, depending on the used tools, by adding a prefix to the name. For example, we can see chr[1-22,X,Y]
for the One Thousand Genomes Project. It is known that this is a chromosome, it is no needed to add any prefix for each variant. The list of known chromosome prefixes are: chrom, chrm, chr and ch.
Reference/Alternate Trimming and left alignment
Reference and alternate trimming consists on removing the trailing (right trimming) and leading (left trimming) bases that are identical in both alleles.
Left aligning a variant means shifting the start position of that variant to the left while keeping the same alleles length till it is no longer possible to do so.
Right and Left trimming
chr1 100 CTC CCC
chr1 101 T C
Indels and empty alleles
Variants in OpenCB does not require any "context base", i.e. allows empty alleles for reference or alternate. Insertions and deletions are represented with an empty alleles for the reference or alternate.
Deletion of one base T
at position 101 chr1 100 AT A chr1 101 TC C
chr1 101 T -
Insertion of one C
at position 201 (between 200 and 201) chr1 200 G GC chr1 201 A CA
chr1 201 - C
Ambiguous trimming and left alignment
It may happen that, in case of deletion or insertion in a region of repeated nucleotides, the trimming operation can be done in multiple ways, and determining the position of the INDEL is ambiguous. In this example we can find that there are four possible ways for normalize the variant:
chr1 100 CTCTCA CTCA
chr1 100 CT -
chr1 101 TC -
chr1 102 CT -
chr1 103 TC -
We guarantee the left alignment by performing first the right trimming. This variant will be normalized as:
chr1 100 CT -
Left alignment
In order to make a correct left alignment, we need the whole reference genome. OpenCB does not support this operation, but may be supported in the future.
Genotype encoding
There are, basically, two different ways of representing the genotype alleles, with or without the allele sequence. In the second way, instead of using the allele itself, is used the allele code. A 0 value represents the reference allele of the Variant, and any other value is a 1-based index into the alternate alleles. A dot value will represent a missing value.
Using an encoded version will allow to determine easily when a genotype is reference, homozygous or heterozygous.
- Sort unphased genotype alleles
- Codify alleles
chr1 100 A T A/A T/A A/T T|A T/.
chr1 100 A T 0/0 0/1 0/1 1|0 ./1
Multi-allelic split
- Split multiallelic variants
- Reorder genotypes
chr1 100 A GT:AD T,C 0/0:40,1,0 0/1:19,20,1 2/1:0:20,22
chr1 100 A GT:AD T,C 0/0:40,1,0 0/1:19,20,1 2/1:0,20,22
chr1 100 A GT:AD C,T 0/0:40,0,1 0/2:19,1,20 1/2:0,22,20
Table of Contents:
- No labels