Are there any tools out there that would convert a SAM/BAM file to a gapped multiple sequence alignment of the reads and the reference? I am looking for a text formatted output (like fasta) of this rather than a vizualization tool.
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It is a non trivial task since the SAM/BAM format isn't a multiple sequence alignment but a collection of pairwise alignments to the reference. The problem comes with conflicting inserts.
e.g. Suppose the first insert is between columns 10 and 11. Most reads say there is no insert here, one read says there should a A, another says AT, a third ATG and a forth says TG. How do you align that? Maybe:
--- (most reads)
A--
AT-
ATG
-TG
That was a fairly easy example - but what if there was another group of reads with an insert of C at this point?
My point is the conversion would require doing this kind of realignment for every insert.
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I understand that this is non-trivial and choices have to be made. I was wondering if a trivial converter that mostly assumes single-base insertions and makes the most obvious choices for a multi-base insertions was available.
Are there any aligners present that provide the padding information?
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Originally posted by query View PostAre there any tools out there that would convert a SAM/BAM file to a gapped multiple sequence alignment of the reads and the reference? I am looking for a text formatted output (like fasta) of this rather than a vizualization tool.
As others have pointed out this is only half the problem though. It's not going to get your data aligned better and put P CIGAR operators in. I'm not aware of tools to automatically do this, but I'm sure some must exist.
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