Changes

##if length <math>\ne</math> 0, classify as INDEL

##if length <math>\ne</math> 0, classify as INDEL

###if shorter allele is of length 1

###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 does not match either of the end nucleotides of the longer allele, add SNP classification

###if shorter allele length > 1

###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)

####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 all nucleotides differ, add MNP classification

#####if not all nucleotides differ, classify as CLUMPED

#####if not all nucleotides differ, add CLUMPED classification

#Variant classification is the union of the classifications of each allele present in the variant.

#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.

#If all alleles are the same length, assign MNP to the variant.