Problem with indels

[Daniel Tabas]

I'm working with a vcf file of the arabidopsis 1001 genomes project. When I load it into Tassel I get the following error:

"Error loading: /pathToVcf/myvcf.vcf
java.lang.IllegalStateException:

Error Processing VCF block: Mismatch of alleles.

At Chromosome *, Position *.

Allele ID larger than number of alleles."

The position in the error contains some insertions like this:

1 1 . T TGATATGTAGCGGTTCC,TGATATCTAGCGGTTCC,G,TAATATGTACCTGTTCC,TGATATATAGCGGTTCC,TGATATGTAGCAGTTCC 40 PASS DP=1000 GT ./. 0/0 5/5 ...

I've changed the genotype information to choose the first insertions, and I finally can load the vcf into Tassel, but the information in the Tassel table is wrong. 

Is there any problem when putting multiple indels in one vcf line?

I use Debian wheezy and the latest release of Tassel 5 stand-alone.

[Ankita Mishra]

Dear, Daniel Tabas.

I am facing the same problem what you faced 2 years back, did you got the solution please help me out because I am stucked.

Thanks

[Ryan Disney]

I have the same error. Did either of you find a solution?

Thanks,

Ryan

[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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