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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

I can't make FastaAlternateReferenceMaker works

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    Genevieve Brandt (she/her)

    Hi Luca Stefanucci, can you try running this with your output ending with .fasta? 

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    Louis Bergelson

    Hi Luca Stefanucci,

    This was a known bug in version 4.1.0.0.  It's been fixed in recent versions.  Please upgrade and try with 4.1.8.0.

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    Luca Stefanucci

    Hi Louis Bergelson,

    Thanks for your answer,

    I am working on HPC and I'd like to use one of the versions which is already installed. Do you know if any of the following works ok fo FastaAlternateReferenceMaker:

    gatk/3.1        gatk/3.3        gatk/3.7.0      gatk/4.1.0.0

    gatk/3.1-1      gatk/3.5        gatk/4.0.alpha 

    gatk/3.2        gatk/3.7        gatk/4.0.beta 

    Thanks,
    Luca

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    Louis Bergelson

    I would really recommend you install the newest version of GATK if you can.  In general 4.1.0.0 should be ok, but it has a bug in FastaAlternateReferenceMaker which wasn't fixed until 4.1.5.0.  (I believe the bug only manifests when there is another error condition that occurs.  I would check that your file paths are right and your vcf looks ok.)  

    If you need to run this particular tool and you can't upgrade to a newer version you'll have to try it in 3.7 I think. 

    I do recommend you try to move to a newer version though since we've made a lot of improvements in the past year and a half.

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