Error: not valid known dog vcf file when using VariantRecalibrator

nonstopnonstop PhiladephniaMember

Hello, I am working on dog targeted sequencing data. In VQSR step, I got error as below. For the record, I use canFam3.fa (from UCSC hg19) as reference and Canis_familiaris.newchr.vcf (Ensembel) as reource file, the two files didn't get error in previous steps. Did anyone have similar problem, Thanks for tips !

INFO 18:07:03,352 HelpFormatter - --------------------------------------------------------------------------------
INFO 18:07:03,355 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
INFO 18:07:03,355 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 18:07:03,355 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 18:07:03,359 HelpFormatter - Program Args: -T VariantRecalibrator -R canFam3.fa -input ./variant_calling/FGC0805.target.raw.snps.indels.vcf -resource:dbsnp,known=false,training=true,truth=false,prior=12.0 Canis_familiaris.newchr.vcf -an DP -an QD -an FS -an MQRankSum -an ReadPosRankSum -mode SNP -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 -recalFile ./variant_calling/FGC0805.target.recalibrate.SNP.recal -tranchesFile ./variant_calling/FGC0805.target.recalibrate.SNP.tranches -rscriptFile ./variant_calling/FGC0805.target.recalibrate.SNP.plots.R
INFO 18:07:03,363 HelpFormatter - Executing as wangfan1@bioapps on Linux 2.6.32-358.14.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_65-b17.
INFO 18:07:03,364 HelpFormatter - Date/Time: 2014/12/02 18:07:03
INFO 18:07:03,364 HelpFormatter - --------------------------------------------------------------------------------
INFO 18:07:03,364 HelpFormatter - --------------------------------------------------------------------------------
INFO 18:07:04,430 GenomeAnalysisEngine - Strictness is SILENT
INFO 18:07:05,183 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 18:07:06,187 GenomeAnalysisEngine - Preparing for traversal
INFO 18:07:06,217 GenomeAnalysisEngine - Done preparing for traversal
INFO 18:07:06,218 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 18:07:06,219 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 18:07:06,219 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 18:07:06,231 TrainingSet - Found dbsnp track: Known = false Training = true Truth = false Prior = Q12.0
INFO 18:07:36,226 ProgressMeter - Starting 0.0 30.0 s 49.6 w 100.0% 30.0 s 0.0 s

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.3-0-g37228af):
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: Invalid command line: No truth set found! Please provide sets of known polymorphic loci marked with the truth=true ROD binding tag. For example, -resource:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmapFile.vcf
ERROR ------------------------------------------------------------------------------------------
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