Problem running SortGenotypeFilePlugin

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ch...@cornell.edu

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Dec 2, 2016, 5:00:31 PM12/2/16
to TASSEL - Trait Analysis by Association, Evolution and Linkage
Hi,

I am having an issue running SortGenotypeFilePlugin on a VCF file that was created by an alternative variant calling pipeline (GATK pipeline). There seems to be an issue with having an asterisk in the alternate allele field. Please see the debug file attached.

Thanks,

Chris


debug.txt
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