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Jonn Smith

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Latest activity by Jonn Smith
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    Jonn Smith commented,

    Please make a new issue in the GATK github with this information.   https://github.com/broadinstitute/gatk

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    Jonn Smith commented,

    Hi khushi ahuja,     Oncotator is no longer supported.  There is an hg19 data sources release somewhere for it, but I no longer know where it is hosted.  Funcotator uses an older MAF spec, which ma...

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    Jonn Smith commented,

    Official comment

    Rami Kheireddine  Funcotator is designed for users to create their own datasources to annotate their own favorite species and genes / other markers.  The pre-packaged datasources are only for human...

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    Jonn Smith commented,

    Manuel Sérgio Sokolov Ravasqueira The chain file you linked does actually contain mappings for `Y` and `MT`. The article I wrote about the reference discrepancies can also be referenced: https://ga...

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    Jonn Smith commented,

    Bhavneet Bhinder - The quickest thing I can suggest is to run Funcotator in `all transcripts` mode (`--transcript-selection-mode ALL`).  This will give you every transcript annotation for all of yo...

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    Jonn Smith commented,

    Official comment

    Hi Zhan, The default is 2 bases.  It looks like this argument was never exposed to the user, so currently there is no way to configure it at runtime (this is a bug!).   I'll add an issue in the GAT...

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    Jonn Smith commented,

    Lim Chen We recommend that people create new posts in the general comments section for support questions. That said, I'm guessing your VCF is aligned to HG19 / B37.  VCF files have header rows in t...

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    Jonn Smith commented,

    Just seeing this now.  Here are up-to-date links since I cannot readily edit this article: https://gatk.broadinstitute.org/hc/en-us/articles/360035889931-Funcotator-Information-and-Tutorial https:...

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    Jonn Smith commented,

    A little while ago we migrated our data to different locations.    https://storage.cloud.google.com/genomics-public-data/references/b37/Homo_sapiens_assembly19.fasta.gz   We no longer have a fasta ...

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    Jonn Smith commented,

    Official comment

    Tjitske - I responded to your github post, but in case you didn't see it:   @Tjitskedv Typically we ask people make a new issue in github or create a forum post, rather than commenting on open pull...