Add alignment rules to place indels correctly

seppinho / haplogrep-cmd

HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.

https://haplogrep.i-med.ac.at/

MIT License

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Closed seppinho closed 5 years ago

seppinho commented 5 years ago

Different alignment strategies for indels exist: 3′ alignment or "right aligned" in the field of forensics vs 5' alignment or "left aligned" in field of medical studies/genetics.
For some haplogroups (e.g. 8281d-8289d) correct indels are necessary to get the best hit.
Idea: Fix indels to 3' (since Phylotree is designed that way).
Introduce new optional parameter (--applyAlignmentRules) to fix misplaced alignments

seppinho commented 5 years ago