VariantRecalibrator input file error

[desmo]

Hi everyone,
I'm having some trouble with the variant quality score recalibrator.
I have the following error message.

MESSAGE: Bad input: Values for HaplotypeScore annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations.

I've used the following command line:
java -jar GenomeAnalysisTK.jar
-T VariantRecalibrator
-resource: hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf
-resource: omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf
-resource: dbsnp,known=true,training=false,truth=false,prior=8.0 dbsnp_132.b37.vcf
-an HaplotypeScore
-nt 3
-input realigned.vcf
-R chr01.fa
-recalFile output.recal
-tranchesFile output.tranches
-rscriptFile output.plots.R

The realigned.vcf file looks like

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Campione
1 565006 . T C 10.43 LowQual AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;HRun=2;HaplotypeScore=0.0000;MQ=60.00;MQ0=0;QD=10.43 GT:AD: DP:GQ:PL 1/1:0,1:1:3.01:40,3,0
1 566933 . A G 11.01 LowQual AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;HRun=2;HaplotypeScore=0.0000;MQ=60.00;MQ0=0;QD=11.01 GT:AD: DP:GQ:PL 1/1:0,1:1:3.01:41,3,0
1 566960 . T C 11.01 LowQual AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;HRun=0;HaplotypeScore=0.0000;MQ=60.00;MQ0=0;QD=11.01 GT:AD: DP:GQ:PL 1/1:0,1:1:3.01:41,3,0
1 567002 . T C 68.76 PASS AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=60.00;MQ0=0;QD=22.92 GT:AD: DP:GQ:PL 1/1:0,3:3:9.01:101,9,0
1 567033 . T C 38.66 PASS AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;MQ=60.00;MQ0=0;QD=19.33 GT:AD: DP:GQ:PL 1/1:0,2:2:6.02:70,6,0

It is already annoted.
So where is the problem?
I have to annotate the "resource" files? I downloaded these callset from the GATK resource boundle. Aren't they already annoted?

[kenietz]

Hi there,
yeah i have the same error and a lot of other people as well
Now then it seems that the VCF file which we pass to the command should have in their INFO lines these strings "QD" "HaplotypeScore" "MQRankSum" "ReadPosRankSum" "FS" "MQ". In your case only HaplotypeScore of course. The nice thing is that the VCF provided by GATK and the ones which supposedly we should pass do not contain that info at all

For example in your case you pass:
-resource: hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf

so this file should have "HaplotypeScore" in the INFO section which im sure it doesnt. Not in mine VCF.

So in my case i pass these three VCFs and they should contain the corresponding Key strings but they do not:
dbsnp_135.hg19.vcf
hapmap_3.3.hg19.sites.vcf
1000G_omni2.5.hg19.sites.vcf

The only VCF file which contain all of the annotations is:
NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.vcf

But then how to specify that want to use that one? For the other three there are the strings: hapmap, omni and dbsnp. But what about NA12878? No idea.

So im stuck on that stupid part

Any help is appreciated
Thank you