Imputation

[Yogendra Khedikar]

Hi, 

I am dealing with germplasm lines which are selfer but natural cross pollination do occur. I have GBS data with missing calls. Is it possible to use Impute option in TASSEL 5?

Could you please suggest any other software for imputation?

Thanks and kind regards,
Yogendra 

[Yogendra Khedikar]

[Terry Casstevens]

Please see the impute section in the User Guide.

www.maizegenetics.net/tassel/docs/Tassel5UserGuide.html

[Yogendra Khedikar]

Thanks Terry. I was thinking FILLIN can only be use for highly self-pollinated crop.

The crop I am working is selfer but degree of outcrossing does occur.

-Yogendra

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Thanks and kind regards,
Yogendra P Khedikar
 

[Terry Casstevens]

There is another imputation method in Tassel but not sure if it's
ready or documented yet.

> https://groups.google.com/d/msgid/tassel/CAC2v03k4wvprka19EH%3Da9g%3DbibqDAhdh-BhhNMROhnCd%3DOt7pw%40mail.gmail.com.

[Peter Bradbury]

FSFHap is a method that is only available from the command line currently, but will be add to the GUI version when the next TASSEL build is posted. However, that method only works for bi-parental populations with inbred parents.

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[yogendra khedikar]

Hi,

Do you mean FILLIN is not yet ready to use using command line version? 

-Yogendra

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[Yogendra Khedikar]

Hi Terry,

Can I use FILLIN using command line version?

-Yogendra

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[Jeff Glaubitz]

Yes, you can.

 

Jeff

 

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Jeff Glaubitz

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[Yogendra Khedikar]

Thanks.

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Thanks and kind regards,
Yogendra P Khedikar
 

[Yogendra Khedikar]

Hi Terry,

Do I need reference panel to impute data using FILLIN?

-Yogendra

[Peter Bradbury]

No. Be sure to read the Tassel 5 user document. The first step is to impute haplotypes. You want to use as many individuals as possible for that step. You will want to include all of the individuals you want to impute as well as any others available.

Peter

[Yogendra Khedikar]

Thanks. I was trying GUI TASSEL 5 using tassel tutorial dataset (mdp_genotype.hmp.txt) but getting following error while generating haplotypes.

Filter Genotype Table: Int start site 933 is longer than end site:932

Thanks,

Yogendra

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[Yogendra Khedikar]

Thanks. I was trying FILLIN in GUI TASSEL 5 using tutorial dataset (mdp_genotype.hmp.txt) but getting following error while generating haplotypes.

Filter Genotype Table: Int start site 933 is longer than end site:932. I am getting similar error with actual dataset as well.

Thanks,

Yogendra

On Tue, Aug 5, 2014 at 2:37 PM, Peter Bradbury <pj...@cornell.edu> wrote:

No. Be sure to read the Tassel 5 user document. The first step is to impute haplotypes. You want to use as many individuals as possible for that step. You will want to include all of the individuals you want to impute as well as any others available.

Peter

On Tuesday, August 5, 2014 3:53:19 PM UTC-4, yogendra khedikar wrote:

Hi Terry,

Do I need reference panel to impute data using FILLIN?

-Yogendra

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Thanks and kind regards,
Yogendra P Khedikar
 

[Peter Bradbury]

I tried using FILLIN with the TASSEL 5 GUI on mdp_genotype.hmp.txt from the tutorial data for TASSEL 5. I was not able to duplicate the problem. The imputation ran quickly but did not actually impute much of the missing data. That is understandable given the relatively small number of SNPs (for maize) and relatively few taxa. A couple of hundred lines does not do a very good job of sampling existing haplotypes in a diverse population.

Peter 

[Yogendra Khedikar]

I tried with 19K snps with 300 lines. I  could extract haplotypes by FILLIN but got error "null" after running second plug in (Impute by FILLIN) 

How many germplasm lines and SNP should be used to impute missing data using FILLIN?

Could you please share example file which can work with FILLIN?

Thanks,

Yogendra  

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[Ruijuan li]

Hi, Yogendra,

I also got "null" for the second plugin (impute by FILLIN). Did you figure out how to fix that?