Root mean square of the mapping quality of reads across all samples (MQ)

Category Variant Annotations

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Overview

Root Mean Square of the mapping quality of reads across all samples.

This annotation provides an estimation of the overall mapping quality of reads supporting a variant call, averaged over all samples in a cohort.

The raw data format for this annotation consists of a list of two entries: the sum of the squared mapping qualities and the number of reads across variant (not homRef) genotypes

Statistical notes

The root mean square is equivalent to the mean of the mapping qualities plus the standard deviation of the mapping qualities.

Related annotations

• MappingQualityRankSumTest compares the mapping quality of reads supporting the REF and ALT alleles.

RMSMappingQuality specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s)	Default value	Summary
Optional Tool Arguments
--allow-old-rms-mapping-quality-annotation-data	false	Override to allow old RMSMappingQuality annotated VCFs to function

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

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--allow-old-rms-mapping-quality-annotation-data

Override to allow old RMSMappingQuality annotated VCFs to function

boolean  false

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GATK version 4.2.2.0-SNAPSHOT built at Thu, 19 Aug 2021 09:49:28 -0700.