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VQSR for indels

pedropedro Posts: 1Member
edited January 2013 in Ask the GATK team

Hello,

I am running Variant Quality Score Recalibration on indels with the following command.

java -Xmx8g -jar /raid/software/src/GenomeAnalysisTK-1.6-9-g47df7bb/GenomeAnalysisTK.jar \
    -T VariantRecalibrator \
    -R /raid/references-and-indexes/hg19/bwa/hg19_lite.fa \
    -input indel_output_all_chroms_combined.vcf \
    --maxGaussians 4 -std 10.0 -percentBad 0.12 \
    -resource:mills,known=true,training=true,truth=true,prior=12.0  /raid/Merlot/exome_pipeline_v1/ref/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf \
    -an QD -an FS -an HaplotypeScore -an ReadPosRankSum  \
    --ts_filter_level 95.0 \
     -mode INDEL \
    -recalFile /raid2/projects/STFD/indel_output_7.recal \
    -tranchesFile /raid2/projects/STFD/indel_output_7.tranches \
    -rscriptFile /raid2/projects/STFD/indel_output_7.plots.R

My tranches file reports only false positives for all tranches. When I run VQSR on SNPS, the tranches have many true positives and look similar to other tranch files reported on this site. I am wondering if anyone has similar experiences or suggestions?

Thanks

Post edited by Geraldine_VdAuwera on

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