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, 08:36, 2 October 2014
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| = Classification Procedure = | | = Classification Procedure = |
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− | ;1. Trim each allele
| + | #Trim each allele with respect to the reference sequence individually |
− | ;2. Inspect length to define INDEL and count insertions or deletions
| + | #Inspect length, defined as length of alternate allele minus length of reference allele. |
− | ;3. Inspect overlapping fragments to count transitions and transversions
| + | ##if length = 0 |
− | : a. if shorter allele is of length 1, check overlap on both ends,
| + | ###if length(ref) = 1 and nucleotides differ, classify as SNP |
− | : if one of the ends match, ignore ts/tv counts.
| + | ###if length(ref) > 1 |
− | : else, align strictly on 5' end and count transitions and transversions.
| + | ####if all nucleotides differ, classify as MNP |
− | : b. If all overlapping nucleotides do not match, assign SNP if shorter allele is of length 1 and MNP if not.
| + | ####if not all nucleotides differ, classify as CLUMPED |
− | : else assign CLUMPED
| + | ##if length <math>\ne</math> 0, classify as INDEL |
− | ;4. Variant classification is the union of the classifications of each allele.
| + | ###if shorter allele is of length 1 |
− | ;5. If all alleles are the same length, assign MNP to the entire variant.
| + | ####if shorter allele does not match either of the end nucleotides of the longer allele, classify as SNP |
| + | ###if shorter allele length > 1 |
| + | ####compare the shorter allele sequence with the subsequence in the 5' end of the longer allele |
| + | #####if all nucleotides differ, classify as MNP |
| + | #####if not all nucleotides differ, classify as CLUMPED |
| + | #Variant classification is the union of the classifications of each allele present in the variant. |
| + | #If all alleles are the same length, assign MNP to the variant. |
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| = Examples = | | = Examples = |