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Indels Recalibration error message
I am trying to recalibrate my VCF files for Indels calling using the below command lines:
java -Xmx2G -jar ../GenomeAnalysisTK.jar -T VariantRecalibrator \
-R ../GATK_ref/hg19.fasta \
-input ./Variants/gcat_set_053_2.raw.snps.indels.vcf \
-nt 4 \
-resource:mills,known=false,training=true,truth=true,prior=12.0 ../GATK_ref/Mills_and_1000G_gold_standard.indels.hg19.vcf \
-resource:dbsnp,known=true,training=false,truth=false,prior=2.0 ../GATK_ref/dbsnp_137.hg19.vcf \
-an DP -an FS -an ReadPosRankSum -an MQRankSum \
--maxGaussians 4 \
-percentBad 0.05 \
-minNumBad 1000 \
-mode INDEL \
-recalFile ./Variants/VQSR/gcat_set_053_2.indels.vcf.recal \
-tranchesFile ./Variants/VQSR/gcat_set_053_2.indels.tranches \
-rscriptFile ./Variants/VQSR/gcat_set_053_2.indels.recal.plots.R > ./Variants/VQSR/IndelRecal2-noAnnot.log
I got this error message, even after taking the recommendation (e.g. maxGaussians 4, --percentBad 0.05). What does this error message mean? my files have too few variants? It's exome-seq.
##### ERROR MESSAGE: NaN LOD value assigned. Clustering with this few variants and these annotations is unsafe. Please consider raising the number of variants used to train the negative model (via --percentBadVariants 0.05, for example) or lowering the maximum number of Gaussians to use in the model (via --maxGaussians 4, for example)