Do BQSR ignore VCF sites marked as filtered, or must they be removed from the file?
I would like to resurrect the issue described here which was never answered definitely:
"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
This is a very old post and since then we have had many versions of GATK. Please upgrade to the latest version and post the tools that you used, version, exact commands and records of problematic variants so we can troubleshoot the issue.
Hi, thank you for your reply. There is no troubleshooting required. The question is whether the BQSR tool ignores variants that are filtered or not.
You will need to remove variants using SelectVariants. I don't think
BaseRecalibratorignores variants marked as filtered.
Sorry about misunderstanding your question. I hope this helps.
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