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Variant classification

471 bytes added, 17:25, 5 September 2014
Definitions
;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
: 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 =
1,102
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