Flair fusion with pbmm2

[fransueturner]

I have a large isoseq dataset that I have already aligned to the genome with pbmm2. I want to try flair fusion. Can use my existing bam files to create a chimeric bam file, or would I have to run flair align for this?

[cafelton]

No you can generate them yourself. Here's a python code snippet I've used.

for file in files:
        infile = pysam.AlignmentFile(f'file', 'rb')
        outfile = pysam.AlignmentFile(file.split('.bam')[0] + '.genomealigned.chim.bam', 'wb', template=infile)
        for align in infile:
            if align.is_mapped and not align.is_secondary:
                if align.has_tag('SA'):
                    outfile.write(align)
        infile.close()
        outfile.close()
        pysam.index(file.split('.bam')[0] + '.genomealigned.chim.bam')