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Variant classification

21 bytes added, 10:31, 2 October 2014
Classification Procedure
##if length <math>\ne</math> 0, classify as INDEL
###if shorter allele is of length 1
####if shorter allele does not match either of the end nucleotides of the longer allele, classify as add SNP classification
###if shorter allele length > 1
####compare the shorter allele sequence with the subsequence in the 5' end of the longer allele (count ts and tv too)
#####if all nucleotides differ, classify as add MNPclassification#####if not all nucleotides differ, classify as add CLUMPEDclassification
#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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