Using Variant Annotator

delangel

2 SNPs with significant strand bias

Several SNPs with excessive coverage

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

Introduction

In addition to true variation, variant 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.

Description of the haplotype score annotation

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 the FAQ article on 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. But 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.

Kurt

Broken link under the 2nd image: "For a complete, detailed argument reference, refer to the GATK document page here." directs to here; http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_gatk_walkers_annotator_VariantAnnotator.html which no longer exists

Geraldine_VdAuwera

Fixed, thanks for reporting it.

lorania

I can't see any images in Firefox?

Geraldine_VdAuwera

@lorania, the image links are temporarily broken. We'll try to get them back up soon.

Geraldine_VdAuwera

Whoops, sorry for the delay -- the image links are fixed now.

sirmark

I don't understand which walker I must use for these annotation options...

Geraldine_VdAuwera

@sirmark, there are three walkers that can add almost any of these annotations to the data. UnifiedGenotyper and HaplotypeCaller can add most of them during the initial variant calling run. VariantAnnotator can add any of them as a separate annotation run. Please see the documentation for each of these walkers for details on how to specify which annotations you want added and which ones can be used.

tommycarstensen

The advice "When running the tool we recommend that you add the -L argument with the variant rod to your command line for efficiency and speed." is so useful that it almost belongs in the documentation: http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_VariantAnnotator.html

My expected run time went from 4 weeks to 2 hours.

Thanks for posting this advice in bold.

Geraldine_VdAuwera

The -L argument is indeed very useful at many stages; we'll try to highlight these uses better. Thanks for pointing this out.