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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

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AS_RMSMappingQuality Follow

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GATK Team
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Allele-specific root-mean-square of the mapping quality of reads across all samples (AS_MQ)

Category Variant Annotations

Overview

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

This annotation provides an estimation of the mapping quality of reads supporting each alternate allele in a variant call. Depending on the tool it is called from, it produces either raw data (sum of squared MQs) or the calculated root mean square.

The raw data is used to accurately calculate the root mean square when combining more than one sample.

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

Caveat

Uninformative reads are not used in this annotation.

Related annotations

  • RMSMappingQuality outputs a version of this annotation that includes all alternate alleles in a single calculation.
  • MappingQualityRankSumTest compares the mapping quality of reads supporting the REF and ALT alleles.

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GATK version 4.0.4.0 built at 02-47-2019 02:47:54.

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