How To Convert Newbler Output Or Ace To Sam Format?

Question

[Casbon]

Anyone converted the output from Roche's mapper (newbler) output to SAM? There are at least two ways to go: either parsing the 454PairAlign.txt or the ACE output.

glu-genetics claims to go the first way, but I can't get it to work (and I have emailed the author but received no response).

Answer 1

[Michael]

I googled this, but haven't tried it. But the amos tool looks like what you need starting with ace files.

[Casbon]

Unfortunately, with the latest release the '-s' option just gives:

/tmp/AMOS/src/Bank/bank2contig: invalid option -- 's'

Not sure if you need to compile it with samtools.

Answer 2

[Casbon]

I couldn't get AMOS to work since their is no SAM output option. I did get glu-genetics to work by checking out the latest code and modifying setup.py not to build the C extensions and fixing the monkey patch 1 2. You can then use

glu seq.Newbler2SAM

It seems to work ok, but the calculation of mapping qualities is definitely not optimal, being either 1 or 60.