Hi,
Should it be possible to run the VariantRecalibrator directly on a set of GVCF files without performing the GenotypeGVCF step (i.e; can I already start Variant Recalibration step 1, while the GenotypeGVCF is running, by using the indivudual GVCF files)? I annotated the GVCF files with VariantAnnotator for QualByDepth, and the fields are present in the files. Nevertheless, VariantRecalibration crashes with the following user error, indicating it can not find the (existing) QD fields in the GVCF files.
ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.6-0-g89b7209):
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 https://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 QD annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations.
ERROR ------------------------------------------------------------------------------------------
I also tried to remove all the reference blocks using gvcftools extract_variants, but that didn't help. The commandline:
/opt/software/sun-jre-8/bin/java -Djava.io.tmpdir=/tmp -Xmx10g -jar /opt/NGS/binaries/gatk/GATK_3.6.0/GenomeAnalysisTK.jar -nt 8 -S LENIENT -T VariantRecalibrator -R /opt/NGS/References/hg19/samtools/0.1.19/hg19.fasta -mode SNP -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -recalFile VQSR.Results/151105_SNL167_0217_C88DPACXX_validation.SNP.vcf -tranchesFile VQSR.Results/151105_SNL167_0217_C88DPACXX_validation.SNP.tranches -rscriptFile VQSR.Results/151105_SNL167_0217_C88DPACXX_validation.SNP.R -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /opt/NGS/References/hg19/gatk_bundle/hapmap_3.3.hg19.vcf -resource:omni,known=false,training=true,truth=false,prior=12.0 /opt/NGS/References/hg19/gatk_bundle/1000G_omni2.5.hg19.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /opt/NGS/References/hg19/gatk_bundle/dbsnp_137.hg19.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 /opt/NGS/References/hg19/gatk_bundle/1000G_phase1.snps.high_confidence.hg19.vcf -input '104689.haplotypecaller.vcf' -input '104690.haplotypecaller.vcf' -input '104691.haplotypecaller.vcf' -input '105376.haplotypecaller.vcf' -input '106892.haplotypecaller.vcf' -input '106893.haplotypecaller.vcf' -input '107087.haplotypecaller.vcf' -input '114357.haplotypecaller.vcf' -input '120174.haplotypecaller.vcf' -input '120175.haplotypecaller.vcf' -input '121129.haplotypecaller.vcf' -input '122359.haplotypecaller.vcf' -input '122777.haplotypecaller.vcf' -input '122778.haplotypecaller.vcf' -input '122780.haplotypecaller.vcf' -input '122781.haplotypecaller.vcf' -input '126178.haplotypecaller.vcf' -input '126895.haplotypecaller.vcf' -input '130124.haplotypecaller.vcf' -input '135188.haplotypecaller.vcf' -input '135189.haplotypecaller.vcf' -input '135979.haplotypecaller.vcf' -input '135980.haplotypecaller.vcf' -input '137294.haplotypecaller.vcf' -input '137295.haplotypecaller.vcf' -input '138577.haplotypecaller.vcf' -input '138578.haplotypecaller.vcf' -input '92793.haplotypecaller.vcf' -input '92794.haplotypecaller.vcf' -input '98176.haplotypecaller.vcf' -input '98177.haplotypecaller.vcf'
Before trying any further, I just wanted to make sure it should be possible or not...
Best,
Geert