Tassel standalone VCF import error with missing data coding "."

[Billie Gould]

Hello Tassel Users, I am writing to see if anyone has encountered VCF file import problems in the standalone version of Tassel.
I am currently encountering an error:

" java.lang.IllegalStateException: ImportUtils: readFromVCF: number of allele depth values does not match number of alleles in line: "

The program encounters "." (missing data) for some of the SNPs when it is expecting one value for each allele in the AD field.
Does anyone know if this is a common problem with importing standard VCFs and if there is an easy work around??

[AC]

Hi Billie,

I've run into a similar issue using TASSEL 4's MergeIdenticalTaxaPlugin. Did you ever resolve your problem?

Best,
Ariel

[Ruijuan li]

I also came across the same problem, anyone here knows how to fix this? 

[Molly Cadle-Davidson]

Has this been resolved?  I have the same error using the tassel 4 standalone:

"java.lang.IllegalStateException: ImportUtils: readFromVCF: number of allele depth values does not match number of alleles in line:  "

On Wednesday, January 22, 2014 at 11:37:50 AM UTC-5, Billie Gould wrote:

[idalia claudia rojas barrera]

Hi users,

I have troubles when I convert from HDF5 to VCF, and try again to open the VCF file in TASSEL. I get the error:

"Allele ID larger than number of alleles"

Does anyone  solved this problem? I see that no one answered your question in spite, HDF5 has many bugs.

Thanks,

Idalia

[Terry Casstevens]

Please follow these instructions to get more information.

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf

Best,

Terry

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[Xiaofei Zhang]

Hi,

For some reasons, I have to use Tassel4. 

I have the same issue when I run  -MergeIdenticalTaxaPlugin. Here is my error report:

java.lang.IllegalStateException: ImportUtils: readFromVCF: number of allele depth values does not match number of alleles in line: 46825 taxa number: 0

I deleted this line and then ran the same command. It worked well.

looking at the the data format:

The format of data in 46825 is 0/0:114:114:100:0,255,255

But the right format should be 0/0:415,0:415:100:0,255,255

I do not know why the data format is different in line 46825. It seemed that only this line had the issue. 

Hope it helps to others. Thank you.

Best wishes,

Xiaofei