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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

(How to) Consolidate GVCFs for joint calling with GenotypeGVCFs Follow

4 comments

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    Robert Butler

    The syntax in this is incorrect, a list of comma separated intervals will not work: `--intervals chr20,chr21`

    Instead, it seems like a list file is required?: https://gatk.broadinstitute.org/hc/en-us/articles/360035531852-Intervals-and-interval-lists

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    Junhao Su

    an error occurred when using joint genotyping, seems the -newQual is not a valid option for `GenotypeGVCFs`

    error message:

    A USER ERROR has occurred: -newQual is not a recognized option

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    Jonathan Klonowski

    can you append a gvcf to a previously created gendb database?

     

    for example:

    gatk GenomicsDBImport \
        -V gendb://my_database 
    -V data/gvcfs/mother.g.vcf \ -V data/gvcfs/father.g.vcf \ -V data/gvcfs/son.g.vcf \ --genomicsdb-workspace-path my_database \ --intervals chr20,chr21

    So that you dont have to rerun GenomicsDBImport on all samples each time you have new samples genotyped?

     

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    Sandra Bohn

    I tried this with the intention of combining gVCFs and using SelectVariants (as described in the addendum) with the --concordance flag to extract a set of variants from my gVCFs. However, the output had all missing data for the GT fields, and after some searching I found that SelectVariants does not output the GT field. Is there a way to extract GTs without using the genotyper? My gVCFs were produced by another caller.

    Also, I could not get chr20,chr21 to work either.

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