Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

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

1 comment

  • Avatar
    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.

    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk