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morispi / LEVIATHAN

Linked-reads based structural variant caller with barcode indexing
GNU Affero General Public License v3.0
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Handling missing haplotag barcodes #8

Closed pdimens closed 1 year ago

pdimens commented 1 year ago

Does Leviathan have a routine/process to identify when there is an invalid/missing haplotagging barcode such that it does not consider the BX tag valid?

For example, an invalid haplotagging BX barcode would have 00 in any of the 4 positions, e.g. A00C41B11D94, A00C03B57D00, etc. Does LRez/Leviathan recognize that these are invalid and should not be considered when clustering alignments by presumed BX molecule?

clemaitre commented 1 year ago

Hi,

Yes, LRez checks the validity of all barcodes (see source code here) and indexes only the valid ones. As Leviathan is based on LRez indexes, it has the same behaviour : invalid barcodes are excluded from the analyses. In case of Haplotagging data, a barcode with 00 in any of the 4 positions is considered as invalid.

Best, Claire

pdimens commented 1 year ago

Thank you very much for the clarification and explanation, Claire!

Best, Pavel