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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

HaplotypeCaller - incompatible contigs (one scaffold only)

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    Genevieve Brandt (she/her)

    Hi suzy_bunters,

    Unfortunately it is not possible to get around this error message using intervals. One option could be using Picard tools to revert your bam file to reads and then realigning your reads with this file so that they match. Another option (if you don't mind loosing the contig) would be to use samtools to remove the contig from your BAM. There are various examples on other forums regarding that.

    Sorry that there is not an easier solution!

    Best,

    Genevieve

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    suzy_bunters

    Hi Genevieve Brandt (she/her)

    Thanks so much for your reply.

    I have a couple of follow up questions, if you have the time!

    1) Do you know of any reason why this could have happened, other than the assembly file being altered?

    2) I recently re-called these variants using the same assembly and BCFTools without any problems. I know you can't be expected to be an expert in BCFTools, but do you know why GATK can't overcome this problem when BCFTools can?

    Kind regards,

    Suzanne 

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    Genevieve Brandt (she/her)

    Hi Suzanne,

    I can provide some insight,

    1) There is also a chance that your BAM file was changed, or there was an issue present 2 years ago that you were not aware of and did not address. Did you successfully run HaplotypeCaller 2 years ago?

    2) Yes unfortunately I am not an expert on BCFTools, I do know however that GATK is sometimes more strict than other tools with these errors because we do not like to have anything pass a step and then cause issues later in the pipeline. 

    Best,

    Genevieve

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    suzy_bunters

    No, this is the first time I've tried using GATK. It's very possible there was an issue two years ago that I didn't address - I'd only just started working with WGS and wasn't accustomed to working with these file formats. 

    Not to worry, thank you so much for your help. At least I now know there's no simple solution!

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