What is the best way to re-align a .bam file?
I need to know exactly what reference genome was used to align a file, so I am looking for a way to de-align and re-align an existing .bam.
Could you suggest a correct way to do this? Is my original approach of going from .bam -> .fastq -> .sam -> .bam feasible?
Is there any loss of information?
P.S. At the moment I am using samtools bam2fq.
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ilykos •
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Bazam has been developed precisely for this purpose.
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I used ngs-bits BamToFastq, but bedtools bamToFastq should work just as good for .bam -> .fastq.
I would not expect a loss of information unless you've filtered out unmapped reads from your bam files. Also hard clipping can create a problem - but more knowledgable people may answer better.