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Variant Recalibration

New YorkPosts: 4Member

Hi,

I am running Variant Recalibration on Indels,prior to this I completed Variant Recalibration and ApplyRecalibration on SNPs.
So,the input file is the recalibrated VCF file from Apply Recalibration step of SNP's.

Below is the error I am getting.

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. See http://gatkforums.broadinsti

tute.org/discussion/49/using-variant-annotator

The command I am using for this is :

jre1.7.0_40/bin/java -Djava.io.tmpdir=./rb_2905_VCF/tmp -Xmx2g -jar GenomeAnalysisTK-2.7-4-g6f46d11/GenomeAnalysisTK.jar -T VariantRecalibrator -R dbdata/human_g1k_v37.fasta -input ${input_file} --maxGaussians 4 -resource:mills,known=false,training=true,truth=true,prior=12.0 Mills_and_1000G_gold_standard.indels.b37.vcf resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.vcf - resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_137.b37.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.indels.b37.vcf -an DP -an QD -an FS -an MQRankSum -an ReadPosRankSum -mode INDEL -recalFile$destdir/${input_file%recal.snps.vcf}recal.indel.recal -tranchesFile$destdir/${input_file%recal.snps.vcf}recal.indel.tranches -rscriptFile$destdir/\${input_file%recal.snps.vcf}recal.indel.plots.R

If I remove the options -an DP -an QD -an FS -an MQRankSum -an ReadPosRankSum,then I get this error:

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Answers

• Broad InstitutePosts: 698Member, Administrator, Broadie, Moderator, Dev admin

Hi there,

I see that you've posted 2 errors, and in each one it says:
"Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself."

I'd recommend searching the forum for the solution to this question. I definitely have seen this topic asked and answered in the past.

Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

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