Polymorphism format conversion for new TASSEL

[Seth Murray]

I have used my old sorghum TASSEL files for teaching my graduate level
class for a few years now and with the change to TASSEL 3.0 they
stopped working (import fine but both GLM and MLM give errors). After
reading some of the threads it seems the most likely problem is that
the "Polymorphism" file format is not really supported anymore -
especially given that I have a high number of heterozygous alleles
and both SSR's & SNPs in the same file. There used to be a “Genotype
Converter” button that worked but that seems to have gone away in the
newer versions.

My questions are:
1. Is there an easy program or method to convert my polymorphism data
into a supported format (Hapmap, Plink, Flapjack, Phylip)? IUPAC
would be an easy conversion except for the SSRs?
2. If I am going to spend the time converting my genotype file to one
of these other formats manually, what is the best format considering:
- how long it will take me to convert it
- the legacy of format and if TASSEL will continue to use it
- what can deal best with both heterozygous data & SSR and SNPs in the
same file

Although I can probably rig up some quick conversion in R if
necessary, for my students I try to communicate quick and easy
freeware tools so they can focus on learning the science of breeding
and genetics instead of computer programming; Therefore if the data
formats for input or output are complex that might be a barrier to
their use if converters are not available.

Thanks!

[Edward S Buckler]

Hi Seth-
Good questions. We are moving to the more modern formats of HapMap and
now VCF. TASSEL 4.0 supports unto 14 different polymorphism (plus rare
and missing), so SSRs are part of the future.

So I think we need to see how SSRs would fit into either HapMap and/or
VCF, and then we can provide a direction forward.

Thanks-
Ed

--
Ed Buckler

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[Priya Ranjan]

Is there a tutorial on how to use vcf files? I have 500 VCF files corresponding to each genotype. So do I need to merge all of them before using tassel or can they work without merging.

[Priya Ranjan]

Forgot to add. I am interested in mixed linear model analysis as part of genome wide association study.

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[Terry Casstevens]

Hi Qi,

Do you have code that supports VCF
that you want me to include? Please use
Hapmap for loading into Tassel 4 at this time.
We haven't added support for Plink yet.

Cheers,

Terry


On Fri, Sep 28, 2012 at 2:03 PM, Qi Sun <qi...@cornell.edu> wrote:
> Terry might be able to tell you when Tassel can take in vcf files directly.
> For now, you can probably use vcftools to convert vcf to plink format to
> load into tassel.
>
>
>
> Qi
>
>
>
> From: Priya Ranjan [mailto:pran...@gmail.com]
> Sent: Friday, September 28, 2012 1:07 PM
> To: Qi Sun
>
>
> Cc: Peter James Bradbury; Terry Casstevens
> Subject: Re: [TASSEL-Group] Polymorphism format conversion for new TASSEL
>
>
>
> I have used vcftools package and I am able to merge the vcf files for
> individual genotype files and get a merged vcf file in .gz format.
>
>
>
> Do I need to convert it in some other format before using it? I can share a
> merged file with you but dont think it would be appropriate to post in
> google group. Please let me know if you are interested in looking at it.
>
>
>
> Thanks
>
> Ranjan
>
>
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> On Wed, Sep 26, 2012 at 4:21 PM, Qi Sun <qi...@cornell.edu> wrote:
>
> The Vcftools package has tools for merging (by column) or concatenating (by
> rows) vcf files.
>
>
>
> Qi