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Jonn Smith

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Latest activity by Jonn Smith
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    Jonn Smith commented,

    1. Community
    2. General Discussion
    3. funcotator Warnning message

    Hi mehran fazel Yeah - the issue is your contig names.  The HG38 contig names recognized by funcotator (and standardized in Homo_sapiens_assembly38.fasta are of the format: chr1 chr2 chr3 chr4 chr5...

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    Jonn Smith commented,

    Official comment
    1. Community
    2. General Discussion
    3. funcotator Warnning message

    Hi mehran fazel, When you say chromosome annotation should be correct do you mean the `chr1` vs `1` naming?  Just in case, can you check the `/mnt/rowData/refrence/GRCh38_latest_genomic.dict` file ...

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    Jonn Smith commented,

    1. Community
    2. Non-Human
    3. Annotate using funcotator

    Hi Sam,     The most recent release of GATK (4.5.0.0) has some fixes for funcotator that may have addressed this issue (in particular, the parsing for GTF/GFF3 files was updated).  If you want, you...

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    Jonn Smith commented,

    1. Tool Index
    2. 4.1.4.1
    3. Funcotator

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

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    Jonn Smith commented,

    1. Tool Index
    2. 4.1.4.1
    3. Funcotator

    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
    1. Community
    2. Non-Human
    3. Annotate using funcotator

    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,

    1. Community
    2. Documentation Questions
    3. Converting Reference Genomes from b37 to hg19

    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,

    1. Community
    2. General Discussion
    3. GATK funcotator transcript selection criteria

    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
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    Jonn Smith commented,

    Official comment
    1. Community
    2. Documentation Questions
    3. SPLICE_SITE specification in Funcotator

    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,

    1. Getting Started
    2. Tutorials
    3. Funcotator Information and Tutorial

    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...