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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

Can funcotator remove mutation data from dbsnp



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    David Roazen

    Hi Luo Hao,

    If you want to remove known germline variants from your callset, you can either do this while running a somatic caller such as Mutect2, or post-calling using a tool like SelectVariants. Funcotator itself cannot do this, as it assumes that you've already filtered your callset using one of these other tools.



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    Luo Hao

    Hi David,

    I run Mutect2 before running Funcotator as follows:

    gatk Mutect2 \
    -R $ref/Homo_sapiens_assembly38.fasta \
    -I ${array[0]}.sort.dedup.baserecal.bam \
    --tumor-sample ${array[0]} \
    --germline-resource af-only-gnomad.hg38.vcf.gz \
    --af-of-alleles-not-in-resource 0.0000025 \
    --panel-of-normals 1000g_pon.hg38.vcf.gz \
    --output ${array[0]}.vcf

    gatk FilterMutectCalls \
    -R $ref/Homo_sapiens_assembly38.fasta \
    -V ${array[0]}.vcf \
    -O ${array[0]}.filter.vcf


    I am not sure could the "--germline-resource af-only-gnomad.hg38.vcf.gz" parameter remove the dbsnp site or I need to do something extra?




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    Can Kockan

    Hi Luo Hao , if your intention was to remove germline variants as David previously mentioned, the gnomAD germline resource should work fine. It should even be a more thorough resource than dbSNP in terms of the number of samples, number of variants, better allele frequencies, etc. so you shouldn't need to do anything extra. Of course, if you do see a variant that you believe shouldn't be there, let us know.

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