I was following the GATK pipeline for my patient data to find the germline mutation.
I was okay until the BQSR procedure. ( the output file is patient1.sorted_dupl_realign_recalib.resort.bam)
Then, I am trying to call the variant using haplotype Calller.
(> java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R genome.fa -I patient1.sorted_dupl_realign_recalib.resort.bam -o patient1.g.vcf -ERC GVCF -variant_index_type LINEAR -variant_index_parameter 128000)
So, I finally got the patient1.g.vcf file.
Now, I am trying to do the variant recalibration step.
java -jar GenomeAnalysisTK.jar -nt 16 -T VariantRecalibrator -R genome.fa -input patient1.g.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg19.sites.vcf -resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg19.sites.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.hg19.sites.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg19.vcf -an DP -an QD -an FS -an MQRankSum -mode SNP --maxGaussians 4 -recalFile patietn1.raw.SNPs.recal -tranchesFile patient1.raw.SNPs.tranches -rscriptFile patient1.recal.plots.R
ERROR MESSAGE: Bad input: Values for DP annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations.
I got the error message even though my patient1.g.vcf file have DP annotation. I checked it.
I googled it and check this forum. but I could not solve this problem.
COuld you please help me with this?