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VQST error with no DP annotation

ngs_medicinengs_medicine ILMember
edited July 2015 in Ask the GATK team

Based on GATK document, I have successfully generated raw vcf file. Now I am trying to to the "Variant Quality Score Recalibration (VQSR)" procedure before the annotation.

For this, variantRecalibrator procedure should have been done. For SNP calibaration,

java -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R genome.fa -input 1-WMT.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 -recalFile raw.SNPs.recal -tranchesFile raw.SNPs.tranches -rscriptFile recal.plots.

I have continuously had errors saying that " Values for DP annotation not detected for ANY training variant " " Values for QD annotation not detected for ANY training variant " " Values for FS annotation not detected for ANY training variant ". Even though my input.raw.vcf file has those annotations..

.chrM 150 . T C 13548.77 . AC=2;AF=1.00;AN=2;DP=473;FS=0.000;GQ_MEAN=1419.00;MLEAC=2;MLEAF=1.00;MQ=40.00;MQ0=0;NCC=0;QD=28.64;SOR=1.344 GT:AD: DP:GQ:PL 1/1:0,473:473:99:13577,1419,0
chrM 195 . C T 15178.77 . AC=2;AF=1.00;AN=2;DP=521;FS=0.000;GQ_MEAN=1562.00;MLEAC=2;MLEAF=1.00;MQ=40.43;MQ0=0;NCC=0;QD=29.13;SOR=0.890 GT:AD: DP:GQ:PL 1/1:0,521:521:99:15207,1562,0


I have read a following posting "http://gatkforums.broadinstitute.org/discussion/5537/vqsr-bad-input-values-for-dp-annotation-not-detected-for-any-training-variant-in-the-input-callset"

I have also tested the comparison of vcf file with goldstandard and my vcf file.
The big difference in my case is that there are no overlap.. since currently I am starting with only mitochondira genes. So, my vcf file only have about 44 snps which has no overlap with hapmap vcf file. I have tested with other traning set. most of them do not have an overlap.. Sometime only 1 snps overlap with

I am not sure whether it is a problem or not.
Such case which do not have overlappped snps, can I still apply VariantCalibrator step?

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