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

False negatives in variant evaluation step

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    Genevieve Brandt (she/her)

    Hi Priyadarshini Thirunavukkarasu,

    I am going to move your post into our Community Discussions -> General Discussion topic, as the Germline topic is for reporting bugs and issues with GATK.

    You can read more about our forum guidelines and the topics here: Forum Guidelines.

    Best,

    Genevieve

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    Genevieve Brandt (she/her)

    Hi Priyadarshini Thirunavukkarasu,

    When you say you are seeing more false negatives in this WES study, what are you comparing it to?

    Thank you,

    Genevieve

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    Priyadarshini Thirunavukkarasu

    I compared to the dataset (HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz) from Genome in bottle database

     

    Is there way to check the pipeline which you are following to call and filter variants with an external dataset

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    Genevieve Brandt (she/her)

    I see, yes I would expect that you would have more false negatives than the genome in a bottle truth set. 

    We have another filtering method you could try which can be run on a single sample, CNNScoreVariants. It might work out better than hard filtering, since you don't have enough samples for VQSR. I would recommend trying it out and seeing how the results compare to your hard filtering results.

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