Filter supplementary alignments when reading BAMs, not prefilter

[diekhans]

Supplementary alignments are very useful in understanding issues with the primary alignment while they can cause FLAIR to create spurious models.

It would be good to leave these in the filtered BAM, and have FLAIR discard the supplementary alignments when it is reading the BAM

[cafelton]

FLAIR does not read the bam, it reads the bed, which cannot contain information about supplementary alignments

[cafelton]

I guess maybe we just need to do the filtering in the bam to bed conversion while leaving the original bam. That makes sense

[diekhans]

FLAIR does not read the bam, it reads the bed, which cannot contain information about supplementary alignments

We can always add extra columns to the BED. With bigBed, such BEDs can even be view in the browser. This is referring to flair align dofiltering(), which is filtering and writing a new BAM. It would be nice to not create two BAMs. Junk such, as internal primed reads could be tossed in the minimap2 -> samtools pipeline without writing to disk. Supplemental reads, which are useful for understanding the alignment can be kept without the need to create another BAM. FLAIR only looking at the BED is even better, it could either discard the supplemental reads when creating the BED or flag them in the BED. It would be nice to be able to run flair fusion without redoing an alignment. cafelton ***@***.***> writes:

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cafelton left a comment (BrooksLabUCSC/flair#426) FLAIR does not read the bam, it reads the bed, which cannot contain information about supplementary alignments -- Reply to this email directly or view it on GitHub: #426 (comment) You are receiving this because you authored the thread. Message ID: ***@***.***>