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Variant Annotator not annotating MappingQualityRankSumTest and ReadPosRankSumTest for INDELs

TechnicalVaultTechnicalVault Sanger, Cambridge, UKPosts: 68Member

Hi,

I'm attempting to use Variant Annotator to annotate some VCFs produced by samtools so I can run VQSR on them. Unfortunately I've gottent stuck and I'm trying to figure out why Variant Annotator wouldn't be annotating INDELs with MappingQualityRankSumTest and ReadPosRankSumTest, it seems to annotate SNPs fine. There are both Homs and het's called on the sample. Could it be I need to left align the indels to get enough coverage? What would you suggest is the best way to debug this? Is there a way to make GATK behave more verbosely about why it's refusing an annotation?

Thanks Martin

Martin Pollard, Human Genetics Informatics - Wellcome Trust Sanger Institute

Best Answers

Answers

  • KurtKurt Posts: 148Member ✭✭✭

    Not sure why they are not annotating, but in regards to making GATK more verbose, have you already added -l DEBUG to your command line?

  • TechnicalVaultTechnicalVault Sanger, Cambridge, UKPosts: 68Member

    Thanks for the suggestion, -l DEBUG does make matters more verbose, but it appears there's no debugging output from the annotator itself. I've now tried running left align then annotating, still flummoxed.

    Martin Pollard, Human Genetics Informatics - Wellcome Trust Sanger Institute

  • TechnicalVaultTechnicalVault Sanger, Cambridge, UKPosts: 68Member
    edited November 2012

    Hmm also they seem to all be coming out with FS=0.000;HaplotypeScore=0.0000.

    If it helps this is the command line used:

    java -Xmx2000m -Xms2000m -server -XX:+UseSerialGC -jar /nfs/users/nfs_m/mercury/src/GenomeAnalysisTK-1.6/GenomeAnalysisTK.jar -T VariantAnnotator -R /lustre/scratch111/resources/vrpipe/ref/Homo_sapiens/1000Genomes/human_g1k_v37.fasta -I /lustre/scratch111/projects/helic/vcf_intermediate-2/lists/chr1-pooled.list --variant /lustre/scratch111/projects/helic/vcf_intermediate-2/pooled/1/1:14000001-15000000.samtools.vcf.gz -L 1:14000001-15000000 -A QualByDepth -A HaplotypeScore -A MappingQualityRankSumTest -A ReadPosRankSumTest -A FisherStrand -A InbreedingCoeff -A DepthOfCoverage -o /lustre/scratch111/projects/helic/vcf_intermediate-2/pooled/1/1:14000001-15000000.vcf.gz.part.vcf.gz
    
    Post edited by TechnicalVault on

    Martin Pollard, Human Genetics Informatics - Wellcome Trust Sanger Institute

  • TechnicalVaultTechnicalVault Sanger, Cambridge, UKPosts: 68Member
    edited November 2012

    My bad that was the command line from the older directory:

    java -Xmx2500m -Xms2500m -server -XX:+UseSerialGC -jar /nfs/users/nfs_m/mercury/src/GenomeAnalysisTK-2.2/GenomeAnalysisTKLite.jar -T VariantAnnotator -R /lustre/scratch111/resources/vrpipe/ref/Homo_sapiens/1000Genomes/human_g1k_v37.fasta -I /lustre/scratch111/projects/helic/vcf_intermediate-3/lists/chr1-pooled.list --variant /lustre/scratch111/projects/helic/vcf_intermediate-3/pooled/1/1:14000001-15000000.samtools.vcf.gz -L 1:14000001-15000000 -U LENIENT_VCF_PROCESSING -A QualByDepth -A HaplotypeScore -A MappingQualityRankSumTest -A ReadPosRankSumTest -A FisherStrand -A InbreedingCoeff -A DepthOfCoverage -o /lustre/scratch111/projects/helic/vcf_intermediate-3/pooled/1/1:14000001-15000000.vcf.gz.part.vcf.gz
    

    Rather than being 0 FS and HaplotypeScore are simply missing from the 2.2 annotated BAMs, similar to ReadPosRankSumTest and MappingQualityRankSumTest. Is the new functionality in the Lite GATK or just in Full?

    Post edited by TechnicalVault on

    Martin Pollard, Human Genetics Informatics - Wellcome Trust Sanger Institute

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