VariantAnnotator

From GSA

VariantAnnotator

For a complete, detailed argument reference, refer to the GATK document page here.

Introduction

In addition to true variation, SNP-callers emit a number of false-positives. Some of these false-positives can be detected and rejected by various statistical tests. VariantAnnotator provides a way of annotating variant calls as preparation for executing these tests.

Examples of Available Annotations

The list below is not comprehensive. Please use the --list argument to get a list of all possible annotations available. Also, see Understanding the Unified Genotyper's VCF files for a description of some of the more standard annotations.

• BaseQualityRankSumTest (BaseQRankSum)
• DepthOfCoverage (DP)
• FisherStrand (FS)
• HaplotypeScore (HaplotypeScore)
• MappingQualityRankSumTest (MQRankSum)
• MappingQualityZero (MQ0)
• QualByDepth (QD)
• ReadPositionRankSumTest (ReadPosRankSum)
• RMSMappingQuality (MQ)
• SnpEff: Add genomic annotations using the third-party tool SnpEff with VariantAnnotator

Note that technically the VariantAnnotator does not require reads (from a BAM file) to run; if no reads are provided, only those Annotations which don't use reads (e.g. Chromosome Counts) will be added. Most Annotations do require reads. When running the tool we recommend that you add the -L argument with the variant rod to your command line for efficiency and speed.