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Variant classification

281 bytes added, 07:36, 2 October 2014
Classification Procedure
= Classification Procedure =
;1. #Trim each allelewith respect to the reference sequence individually;2#Inspect length, defined as length of alternate allele minus length of reference allele. Inspect ##if length = 0###if length to define INDEL (ref) = 1 and count insertions or deletionsnucleotides differ, classify as SNP###if length(ref) > 1 ####if all nucleotides differ, classify as MNP####if not all nucleotides differ, classify as CLUMPED;3. Inspect overlapping fragments to count transitions and transversions##if length <math>\ne</math> 0, classify as INDEL: a. ###if shorter allele is of length 1, check overlap on both ends, : ####if one shorter allele does not match either of the ends matchend nucleotides of the longer allele, ignore ts/tv counts.classify as SNP ###if shorter allele length > 1: else, align strictly on ####compare the shorter allele sequence with the subsequence in the 5' end and count transitions and transversions.of the longer allele: b. If #####if all overlapping nucleotides do not matchdiffer, assign SNP if shorter allele is of length 1 and classify as MNP #####if not.: else assign all nucleotides differ, classify as CLUMPED;4. #Variant classification is the union of the classifications of each allelepresent in the variant.;5. #If all alleles are the same length, assign MNP to the entire variant.
= Examples =
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