Question: BAM Merger Two Separate References?
1
gravatar for glew
5 weeks ago by
glew20
glew20 wrote:

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 • 114 views
ADD COMMENTlink written 5 weeks ago by glew20
2

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?

ADD REPLYlink written 4 weeks ago by hurfdurf480
1

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

ADD REPLYlink written 4 weeks ago by glew20
1

That is not compatible with the BAM specifications. BAM expects a single reference that the coordinate system is based on.

ADD REPLYlink written 5 weeks ago by ATpoint42k
1

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.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by genomax92k
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