BAM Merger Two Separate References?
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9 months ago
glew ▴ 20

Situation:

ReferenceA and ReferenceB are completely different and cannot be merged into single reference. 
Align reads to both A and B.

I want to merge the two bam files where it will score which alignment is better for each read. Does anyone know of how to do this or if there is a tool available for this? Thanks for your help.

alignment Assembly • 361 views
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Why not create a hybrid reference with both Reference A + Reference B in one fasta file. You can then align the data to this reference. You will need to be mindful of multi-mapping (you will need to let the reads map in all possible locations). You could then post process the alignment to find out which reference a read aligns to better.

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Are you asking this because of the index time cost? E.g. you need to add a small minichromosome (different with every sample) to a human index, and the indexing time dwarfs the search time?

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Yes, the indexing time was the main issue I was worried about.

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