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, 18:25, 5 September 2014
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| ;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. |
− | : AND
| |
− | : b. The removal of a subsequence of the longer sequence would reduce the longer sequence to the smaller sequence.
| |
| ;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 = |