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Old 05-14-2010, 12:30 PM   #1
Location: Connecticut

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Default ACE to SAM/BAM pile-up

Hi all,

I'm trying to generate predicted SNP sites using a new program called ACCUSA, but need to get my data into SAM/BAM pile-up format first. I'm going from a 454-data generate ACE file to this format, but first I need to convert that to SAM/BAM format (before I can use SAMTOOLS to do the pileup) and have gotten myself a bit confused about what program to use to do this conversion. Any thoughts out there about what would be a good utility to do this conversion from ACE to SAM/BAM?

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Old 06-16-2010, 04:23 AM   #2
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Location: Graz, Austria

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I would be interested in this conversion too, ACE is by far too big to visualize easily.
I know there is a way of parsing the ACE file in Biopython, but the AlignIO package yet doesn't support SAM-File Output as far as I know.
Really looking forward to standardizing file formats in NGS...
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Old 06-16-2010, 05:40 AM   #3
Location: JHI, Dundee, UK

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If you use the AMOS tools, I believe you can go from ACE to AFG/BANK, and from there to SAM/BAM.

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Old 06-16-2010, 09:39 AM   #4
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Gap5 can import ACE too and can output SAM. Although the SAM flags for 1st/2nd pair are a bit broken in the current release; fixed in the SVN tree. I've no idea how it compares to AMOS for validity or efficiency.

Both of these are around-the-houses solutions though so I'm sure someone must have written a dedicated perl hack for it by now. Anyone?

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