VCF generated by VCFtools (v0.1.13) not readable in TASSEL 5

[Jessica May]

Hi All,
I am using TASSEL5 latest build. Standalone downloaded from:
https://bitbucket.org/tasseladmin/tassel-5-standalone/downloads#tag-downloads

I am trying to load VCF File generated by  VCFtools (v0.1.13) after filtering.

It says error in number of sites for some texa.

I believe everything is fine as PLINK and VCFtools are able to read file.

Any idea?

regards

May

[Terry Casstevens]

Hi Jessica,

Does you file have values ".:.:.:."? We have an open issue regarding
that. I think that should be imported as unknown values. Do you know
if that is true?

You can send me your file privately if you want.

Best,

Terry

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[Jessica May]

Thanks Terry,

I have not peep in to file.

The error what i am getting is that a particular row do not have same number of sites what are expected.
i will try to subset file and send you as it is very big.

regards

May

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[Ginnie M]

Hi,
I'm having a similar issue. I'm using TASSEL5 to convert a HDF5 file into VCF format for use downstream (in Beagle4.0). While the conversion seems to work, Beagle does not approve of TASSEL's notation for deletions:
Exception in thread "main" java.lang.IllegalArgumentException: ALT allele [-] is not a sequence of A, C, T, G, N, or '*' characters
VCF seems to want 'DB' for a deletion (though I'm not sure if Beagle will be happy with this). Is there a line I could change in TASSEL5 to fix/test this?

[Terry Casstevens]

Are you saying Tassel puts - for missing data?

What does VCF consider missing? N, *, DB?

What does Beagle use?

> https://groups.google.com/d/msgid/tassel/3814e12b-2550-47e4-8eab-45b8debcb70c%40googlegroups.com.

[Ginnie M]

Tassel seems to be putting a '-' for what the TASSEL gui codes as '-'/deletion, not missing. VCF and Beagle seem to want, I think, a '.' for the alternate allele when there's a single base deletion. I'm not entirely clear on this--this is just what I'm piecing together (possibly incorrectly).

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