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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

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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    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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    Sinem Selvi

    Based on the information, following variant is homozygous based on FORMAT DP or INFO DP?

    When i check on IGV the variant looks heterozygous with following read counts:
    chr1:228346358;total count 150;ref G count 150;ins count 1.
    chr1:228346359;total count 157;ref C count 157;ins count 80.

    chr1    228346358       .       G       GCCGCCGCGGCCCCCCGGCCT   3040.03 .       AC=2;AF=1.00;AN=2;DP=149;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.51;SOR=2.105      GT:AD:DP:GQ:PL  1/1:0,72:72:99:3054,203,0

    So how to be sure the variant is hom alt or het?
    Thank you

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