From Genome Analysis Wiki
Jump to navigationJump to search
21 bytes added
, 10:31, 2 October 2014
Line 33: |
Line 33: |
| ##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. |