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Variant classification (view source)

Revision as of 08:36, 2 October 2014

281 bytes added ,  08:36, 2 October 2014
→‎Classification Procedure
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= Classification Procedure =
 
= Classification Procedure =
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;1. Trim each allele
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#Trim each allele with respect to the reference sequence individually
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;2. Inspect length to define INDEL and count insertions or deletions
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#Inspect length, defined as length of alternate allele minus length of reference allele.
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;3. Inspect overlapping fragments to count transitions and transversions
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##if length = 0
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:  a. if shorter allele is of length 1, check overlap on both ends,
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###if length(ref) = 1 and nucleotides differ, classify as SNP
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:            if one of the ends match, ignore ts/tv counts.
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###if length(ref) > 1
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:      else, align strictly on 5' end and count transitions and transversions.
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####if all nucleotides differ, classify as MNP
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:  b. If all overlapping nucleotides do not match, assign SNP if shorter allele is of length 1 and MNP if not.
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####if not all nucleotides differ, classify as CLUMPED
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:      else assign CLUMPED
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##if length <math>\ne</math> 0, classify as INDEL
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;4. Variant classification is the union of the classifications of each allele.
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###if shorter allele is of length 1
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;5. If all alleles are the same length, assign MNP to the entire variant.
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####if shorter allele does not match either of the end nucleotides of the longer allele, classify as SNP
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###if shorter allele length > 1
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####compare the shorter allele sequence with the subsequence in the 5' end of the longer allele
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#####if all nucleotides differ, classify as MNP
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#####if not all nucleotides differ, classify as CLUMPED
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#Variant classification is the union of the classifications of each allele present in the variant.
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#If all alleles are the same length, assign MNP to the variant.
    
= Examples =
 
= Examples =
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Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/11679"

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