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Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
Do GATK4 tools ignore VCF sites marked as filtered, or must they be removed from the file?
I think the GATK tools mostly ignore filtered sites (sites without PASS or .)...
Hi, @Sheila ,
Can you confirm that GATK4 tools ignore variants in a VCF that are marked as filtered (i.e. not PASS), but that are still present in the VCF file?
For example, I have a bootstrapped
knownSites.hardFilter.vcf file that I produced with
VariantFiltration with the recommended hard filter parameters. This VCF still includes the filtered variants in the file—it has only marked them as filtered in the
FILTER column. My question is this: Would, for example,
BaseRecalibrator—which takes the
knownSites.hardFilter.vcf as input—ignore the variants in the VCF file that are marked with a filter instead of
PASS in the
FILTER column in the VCF? I need to know if tools like
BaseRecalibrator are actually ignoring variants marked as filtered but that are still present in the VCF file, or if I need to physically remove them using
SelectVariants. Please let me know, thanks.