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Revision as of 18:25, 5 September 2014
, 18:25, 5 September 2014→Definitions
;3. INDEL
;3. INDEL
: a. The reference and alternate sequence are not the same length.
: a. The reference and alternate sequence are not the same length.
;4. CLUMPED
;4. CLUMPED
: a. A clumping of nearby SNPs, MNPs or Indels.
: a. A clumping of nearby SNPs, MNPs or Indels.
;5. SV
;5. SV
: The alternate sequence is represented by a angled bracket tag.
: 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 =
= Examples =
