indels ApplyRecalibration

lvzvialvzvia Member
edited April 2014 in Ask the GATK team

I am trying to set GATK pipeline with version 3.1. Everything went well so far...
Also- SNPs calibration went well. The problem is with applying calibration on indel.
Here are the commands I used (the first was finished successfully, but not the second):

java -jar /home/lvzvia/GATK-3.0/GenomeAnalysisTK.jar -T VariantRecalibrator -R /ngs001/db/gatk_resources/bundle/2.5/b37/human_g1k_v37.fasta -input Combine1.vcf --maxGaussians 4 -resource:mills,known=false,training=true,truth=true,prior=12.0 /ngs001/db/gatk_resources/bundle/2.5/b37/Mills_and_1000G_gold_standard.indels.b37.vcf -an DP -an FS -an ReadPosRankSum -an MQRankSum -mode INDEL -recalFile raw.INDELs.recal -tranchesFile raw.INDELs.tranches -rscriptFile recal.INDEL.plots.R

java -Xmx3g -jar /home/lvzvia/GATK-3.0/GenomeAnalysisTK.jar -T ApplyRecalibration -R /ngs001/db/gatk_resources/bundle/2.5/b37/human_g1k_v37.fasta -input Combine1.vcf -tranchesFile raw.INDELs.tranches -recalFile raw.INDELs.recal -o recal.INDELs.vcf -ts_filter_level 99.9

The error message:

##### ERROR MESSAGE: Encountered input variant which isn't found in the input recal file. Please make sure VariantRecalibrator and ApplyRecalibration were 
run on the same set of input variants. First seen at: [VC input @ 1:14192 Q86.53 of type=SNP alleles=[G*, A] attr={AC=1, AF=0.019, AN=52, BaseQRankSum=-7.3
10e-01, ClippingRankSum=0.731, DP=401, FS=0.000, InbreedingCoeff=-0.0296, MLEAC=1, MLEAF=0.019, MQ=35.30, MQ0=0, MQRankSum=0.731, QD=17.31, ReadPosRankSum=
-7.310e-01} GT=GT:AD:DP:GQ:PL   0/0:.:2:6:0,6,50        0/0:.:2:6:0,6,71        ./.:.:0 0/0:.:2:6:0,6,72 

The input vcf contained both indel and SNPs and it went well for the SNPs.

Post edited by Geraldine_VdAuwera on

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