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Mohammad Deen Hayatu

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Latest activity by Mohammad Deen Hayatu
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    Mohammad Deen Hayatu commented,

    All i had to do was redownload the reference from the GATK website including the dictionary. This is easier of course if youre using the GATK specific reference like b37 etc. If you're using hg19, ...

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    Mohammad Deen Hayatu commented,

    Update.. I finally got it to run by matching my reference to the chain file and also setting WARN_ON_MiSSING_CONTIG=true . I got this warning in the end. WARNING 2022-10-07 09:47:55     LiftoverVcf...

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    Mohammad Deen Hayatu commented,

    Hello Genevieve-Brandt-she-her, The code finally worked when i removed the reference and all the associated dictionaries and redownloaded from the link provided by gatk. However i run into a differ...

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    Mohammad Deen Hayatu created a post,

    Issues with LiftoverVcf

    Answered

    So i am trying to liftover a VCF from hg38 assembly to hg19 using LiftOver tool in picard by i keep running into errors of reference dictionary not present despite having it in the same directory a...