Having problem with VQSR step

AzlinAzlin Member
edited June 2016 in Ask the GATK team

Hi there.

I'm Lynn, doing the whole genome sequencing for human. I'm currently using GATK for variant call and now having problems for VQSR step.

Here is the command I entered:
promise@eden:/media/promise/storage/Tools/Softwares/GenomeAnalysisTK-3.4-0$ java -Xmx4g -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R /media/promise/storage/References/Referance/GATK\ Bundle/hg19/ucsc.hg19.fasta -input /media/promise/storage/Postgrad/Deep\ and\ median\ coverage/Re-run\ phasing/Deep\ coverage/SM19/SM19.bam.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /media/promise/storage/References/Referance/GATK\ Bundle/hg19/hapmap_3.3.hg19.vcf -resource:omni,known=false,training=true,truth=true,prior=12.0 /media/promise/storage/References/Referance/GATK\ Bundle/hg19/2.8/1000G_omni2.5.hg19.sites.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 /media/promise/storage/References/Referance/GATK\ Bundle/hg19/2.8/1000G_phase1.snps.high_confidence.hg19.sites.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /media/promise/storage/References/Referance/GATK\ Bundle/hg19/2.8/dbsnp_138.hg19.vcf -an QD -an MQRankSum -an ReadPosRanksum -an FS -an DP -mode SNP -recalFile /media/promise/storage/Postgrad/Deep\ and\ median\ coverage/Re-run\ phasing/Deep\ coverage/SM19/SM19_snp.recal -tranchesFile /media/promise/storage/Postgrad/Deep\ and\ median\ coverage/Re-run\ phasing/Deep\ coverage/SM19/SM19_snp.tranches -rscriptFile /media/promise/storage/Postgrad/Deep\ and\ median\ coverage/Re-run\ phasing/Deep\ coverage/SM19/SM19_snp.plots.R

It initially run smoothly but then the error appeared:

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.4-0-g7e26428):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Bad input: Values for ReadPosRanksum annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See http://gatkforums.broadinstitute.org/discussion/49/using-variant-annotator
ERROR ------------------------------------------------------------------------------------------

I've tried to find the answer from the forums but I'm not really understand on what should I do with to fix this error. Could anyone please help me?

Thank you in advance!
Lynn.

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