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Variant classification

91 bytes added, 07:43, 2 October 2014
Classification Procedure
#Inspect length, defined as length of alternate allele minus length of reference allele.
##if length = 0
###if length(ref) = 1 and nucleotides differ, classify as SNP (count ts and tv too)
###if length(ref) > 1
####if all nucleotides differ, classify as MNP (count ts and tv too)####if not all nucleotides differ, classify as CLUMPED (count ts and tv too)
##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 SNP
###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 MNP
#####if not all nucleotides differ, classify as CLUMPED
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