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

Allele Depth (AD) is lower than expected Follow

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    Shashank Katiyar

    Thanks, this is a well explained article about a much needed missing information. I wonder if is there any parameter to change the 'difference between the Phred scaled likelihoods' from .2 to the desired number?

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    xie186

    It'll be helpful to report read coverage after filtering for each sample in the output of GenotypeGVCFs

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    Burak Alver

    Thank you for this explanation. This clarifies some questions. However, I continue to be confused.

    The "The explanation: uninformative reads" section of the article suggests that there should sometimes be two different DP values.
    1. DP-info: how many reads cover the position.
    2. DP-format: how many reads are informative to distinguish two different alleles.
    Then, the second type of reads should also be reported in AD, and there sum(AD)=DP-format.

    All this sounds reasonable. But the vcf line example does not agree with this explanation. There, both DP values are 10, and sum(AD)=0.

    Is there a difference between DP-info and DP-format?

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