how to convert hapmap genotype files (hmp.txt) to VCF?

[Paul Tanger]

How do I convert the hapmap files that TASSEL creates into VCF files?

I tried using this plugin from GATK but it doesn't work:

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_VariantsToVCF.html

Any ideas?

Thanks!

[Terry Casstevens]

./run_pipeline.pl -Xmx5g -fork1 -h mdp_genotype.hmp.txt -export
-exportType VCF -runfork1

Or using GUI, import Hapmap and export as VCF.

Cheers,

Terry

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[Paul Tanger]

Thanks.. but this doesn't work with tassel3.  Maybe it was added to tassel 4?

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[Paul Tanger]

Oh Nevermind, I got it to work.. but I never saw this in the tassel 3 documentation.

Thanks!

[Paul Tanger]

Ok, so the command runs in tassel 3, but the file that it produces is just a duplicate of the hapmap file - it is not in VCF format.

So just to clarify, the export plugin works in tassel 4 but NOT tassel 3.

[Carlos Hernando Galeano mendoza]

Hi all,

talking about .vcf files, do you have a script to convert vcf files to genotyping matrix?

Thanks,

Carlos

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451 East Health Science Drive
Davis, CA 95616-8816
Phone (530) 752-8889
Fax (530) 754-9658

[Terry Casstevens]

I'm not sure what you mean by "genotyping matrix". Here is the
command to convert to Hapmap.

./run_pipeline.pl -Xmx5g -fork1 -vcf mdp_genotype.vcf -export
-exportType Hapmap -runfork1

Additional information...

http://www.maizegenetics.net/tassel/docs/TasselPipelineCLI.pdf

Cheers,

Terry

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[Dina]

Hi everyone,

I have tried this command line, and it works. But the vcf generated does not have any quality scores and depth. Is anyone have an idea how to figure it out?

Thanks a lot,

Amandine

[Nick Bell]

Hi Amandine,

I am working on a similar issue- the depth is recorded in a separate file (at least from the UNEAK pipeline that my data came from). There should be a HapMapCount.hmc file which records this data.

There must be a way to use the scores in the count file to build the .vcf file, but I haven't figured it out yet.

However it is worth noting that the count file is capped at 127 hits per allele. So is not informative for loci with very high depth.

[Amandine Cornille]

Hi Nick,

Thanks for your help and mail!

Actually, using the Tassel pipeline, I still did not figure out to do it. But I will check the UNEAK pipeline.

ok, if you find, do not hesitate to let me know, thanks!

best,

Amandine

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Post-doc

Department of Ecology and Genetics

EBC, Uppsala University

Norbyvägen 18D

75236 Uppsala

Sweden

[Edward S. Buckler]

Just as a heads up, the TASSEL GBS pipeline is being migrated to TASSEL 5. The UNEAK pipeline will be made as a 1 step detour out of the reference pipeline. Depth is also been better handled, where exact depth is recorded of <=127, and log estimates with 3% error are being recorded for values up to 20,000 in-depth.

-- 
Ed Buckler

From: Amandine Cornille <amandine...@gmail.com>
Reply-To: "tas...@googlegroups.com" <tas...@googlegroups.com>
Date: Monday, January 20, 2014 at 8:03 AM
To: "tas...@googlegroups.com" <tas...@googlegroups.com>
Subject: Re: [TASSEL-Group] how to convert hapmap genotype files (hmp.txt) to VCF?

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[Amandine Cornille]

Hi Edward,

ok, thanks for the update!

best,

Amandine

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[Christine Lucas]

Terry---

I have no idea if you will get this, as this thread is over 4 years old, but.....using the GUI (TASSEL 5), I cannot figure out how to export my marker data set.hmp.txt as a vcf.  Any suggestions?

Thanks,
Christine  

[Terry Casstevens]

Select the dataset and use File -> Save As...

Then select VCF from drop down

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[Christine Lucas]

Terry--

I tried that already, to no avail.  Unless I am doing something incorrectly.  I selected my dataset (shown below), and tried saving as a vcf, but the only option in the drop down is "Table".  

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[Terry Casstevens]

Your data didn't get imported as genotype data.  Maybe the file doesn't have .hmp.txt extension and didn't guess correctly

You can try File -> Open As...  to explicitly say it's Hapmap

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[Christine Lucas]

You are right.  It was one of the following: one incorrect header, no NAs where there were blank cells, and/or not having the .hmp.txt extension.  I was able to successfully import as sequence data.   

Thank you!!!!!

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[Wardah Mustahsan]

Hi Terry

Is the "export/import" feature no longer available in Tassel GUI ( ver. 5.2.53)? I don't really see it in the top taskbar options.

On Thursday, August 22, 2013 at 10:29:45 PM UTC-5, Terry wrote:

./run_pipeline.pl -Xmx5g -fork1 -h mdp_genotype.hmp.txt -export
-exportType VCF -runfork1

Or using GUI, import Hapmap and export as VCF.

Cheers,

Terry


On Thu, Aug 22, 2013 at 8:26 PM, Paul Tanger <pault...@gmail.com> wrote:
> How do I convert the hapmap files that TASSEL creates into VCF files?
> I tried using this plugin from GATK but it doesn't work:
> http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_VariantsToVCF.html
>
> Any ideas?
>
> Thanks!
>
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[Terry Casstevens]

It is now File -> Open, File -> Save

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[wardah]

Hi Terry

I need to more clarification, how does this help in the conversion of hapmap to vcf or vcf to hapmap

Have a pleasant day!

Wardah Mustahsan

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[Girija Hari]

Hi Chrisin/Terry

I am not sure if I will be able to get an answer to this. I am trying to export merged vcf files into vcf format file. But i am unable to do so with TASSEL UI. Is there any ways I can get this done. I successfully merged 5 vcf files and a merged Genotype Table is created. But how do I import this into a vcf format to my machine for further analysis in R

Best regards

Gimeno

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[Terry Casstevens]

File -> Save As...

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[Girija Hari]

Thanks a lot, yeah I was doing issue with assigning a filename while exporting the vcf file.

Thank you

Best regards

gimeno