BAM Merger Two Separate References?
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.
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That is not compatible with the BAM specifications. BAM expects a single reference that the coordinate system is based on.
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.
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?
Yes, the indexing time was the main issue I was worried about.