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WenyaWang

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Latest activity by WenyaWang
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    WenyaWang commented,

    Hi, Here is the reply from NovoAlign: "Hi Wenya   Thanks for your email.   Yes it does appear that GATK does not like the ambiguous IUPAC base 'M' that exists and it is a known issue that Haplotype...

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    WenyaWang commented,

    Thanks for your suggestion. I followed the instructions in this documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360035891231-Errors-in-SAM-or-BAM-files-can-be-diagnosed-with-Valida...

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    WenyaWang commented,

    Besides that I come up with the same error when I use latest Version.

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    WenyaWang created a post,

    GATK4.1.3.0 HaplotypeCaller ERROR

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    Can you please provide a) GATK version used :4.1.3.0b) Exact GATK commands used : HaplotypeCallerc) The entire error log if applicable. : java.lang.IllegalArgumentException: Unexpected base in alle...