Genome Analysis Toolkit

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

Varinat PASS given Genotype quality = 0

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    Anthony Dias-Ciarla

    Hi Matteo Orlandi,

    Thank you for writing to the GATK forum! I hope that we can help you sort this out.
    After reviewing your post with our developers, I have some feedback to share with you. 

    A variant with a GQ = 0 being PASS is not unexpected. It is clear that there is a variant here, but we won't be able to distinguish its genotype.

    While the mapping quality could be better, this is still a perfectly reasonable variant. Unfortunately, it doesn't have the best allele balance, so we can't tell what the genotype is but this is as expected.

    I hope this helps clear some of your doubts! Thank you again for writing to the GATK forum. Please do not hesitate to reach out if any further questions should arise.

    Best,
    Anthony

     

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    Anthony Dias-Ciarla

    Hi Matteo Orlandi,

    We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!

    Kind regards,

    Anthony​

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