Genome Analysis Toolkit

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

AS_MappingQualityRankSumTest Follow

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    Shin Lin

    I run 

    gatk --java-options "-Xmx10g" VariantAnnotator -R GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta -V /merge_output.clean.gvcf.gz -O merge_output.clean.annot.gvcf.gz -I aligned.sorted.bam -A AS_MappingQualityRankSumTest -A DepthPerSampleHC -A ExcessHet -A MappingQualityRankSumTest -A RMSMappingQuality -A ReadPosRankSumTest

    But I don't get any MQRankSum annotation added to the output.  How is this supposed to work?  Thanks.

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