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Errata: documentation and help text apparently incorrect for ApplyVQSR, --ts_filter_level
Using the command, based on the example from the documentation:
Based on this:
I used the command below:
/saturn/Software/NGS_Software/gatk-126.96.36.199/gatk-188.8.131.52/gatk ApplyVQSR -R /saturn/Software/NGS_Reference/GATK_ref/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -V /saturn/dmurphy/gvcfs/cohortsall.vcf.gz -O output-VQSR.vcf.gz --ts_filter_level 99.0 --tranches-file output.tranches --recal-file output.recal
I get the result
A USER ERROR has occurred: ts_filter_level is not a recognized option
The option is in the current help text from the tool and the example usage.
when checking gatk ApplyVQSR --help it still includes it.
--truth-sensitivity-filter-level,-ts-filter-level:Double The truth sensitivity level at which to start filtering Default value: null.
also, it's apparently not related to the double "-", using "-ts-filter-level" yields
A USER ERROR has occurred: t is not a recognized option
using "--truth-sensitivity-filter-level" it works correctly.