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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:

https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.3.0/org_broadinstitute_hellbender_tools_walkers_vqsr_ApplyVQSR.php

Based on this:

I used the command below:

/saturn/Software/NGS_Software/gatk-4.0.4.0/gatk-4.0.4.0/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.

Answers

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