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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

GenomicsDBImport error from # fields in AS_UNIQ_ALT_READ_COUNT



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    Genevieve Brandt (she/her)

    Hi Jeff Gaither,

    This issue is coming from a bug with the AS_UNIQ_ALT_READ_COUNT. The annotation is not meant for germline use, so you won't need to have it in your file. 

    Here is another issue with that annotation in github, it's currently still open: I commented with your example.

    For the rest of your files, I would recommend not adding this annotation. You can just stick to the standard annotations with -G StandardAnnotation and -G AS_StandardAnnotation in HaplotypeCaller.

    Please let me know if you have any more questions.



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    Jeff Gaither

    Hi Genevieve, 

    Cool, then I'll just cut the AS_UNIQ_ALT_READ_COUNT from future runs. Thanks for your help!

    To anyone coming across this issue, removing the annotation from your VCF is as simple as 

    bcftools annotate -x INFO/AS_UNIQ_ALT_READ_COUNT your.vcf.gz


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    Genevieve Brandt (she/her)

    No problem! Glad we could figure out the issue.

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