Re: [MUMmer-help] MUMmer SNP output data help

[Adam P. <aph...@gm...>]

Hi Ramya,
For draft IonTorrent data, you may be better off using a reference-mapping
approach for SNP calling and work directly from the reads rather than the
assemblies. There are a number of available pipelines for this. By mapping
the reads you could take the quality values of each base into account and
perhaps obtain more accurate SNP calls.

If you are determined to use assemblies, we have a new tool called ParSNP
for comparing multiple samples. Here is the paper if you are interested:
http://www.genomebiology.com/content/15/11/524 That paper also discusses
the tradeoffs between assembly-based and read-based SNP calling.

To directly answer your questions:
1. Yes, but there are probably better options
2. Yes
3. You would align each assembly to the reference individually
4. No, you would have to parse this information yourself from the output

Best,
-Adam


On Wed, Jun 17, 2015 at 8:34 AM, <ra...@bi...> wrote:

> Hi all,
>
> I have been working with Iontorrent platform. I have sequence of a
> bacteria which was obtained by denovo assembly on Ion torrent platform. I
> have to use this data as a reference for calling SNP's across 6 samples. So
> it would be draft genome vs draft genome. I have used the nucmer snp
> caller. My questions are:
>
> 1) can i use this tool for calling SNP's from data generated from
> Iontorrent platform?
>
> 2) Do i need to align the draft sequences first before going to the SNP
> calling option?
>
> 2) Should i cal SNP's from one sample and then compare it with others or
> all the sample's data can be combined and called for SNP's? for example can
> i go with command line
>
> nucmer --prefix=ref_qry ref.fasta sample1.fasta sample2.fasta
> sample.3.fasta
>
> 3) IS there an option to generate unique SNP's to a particular sample and
> common variants across all the samples?
>
> Thanks in advance,
>
>
>
> Ramya.
>
>
>
>
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