error while running VariantRecalibrator
Posted in Ask the GATK team | Last updated on 2012-11-22 01:25:17

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experiment: target enrichment and sequencing using Illumina platform

raw VCF file from UnifiedGenotyper -> Variantrecalibrator

I got the following error, any potential explanation? Thanks

##### **ERROR MESSAGE: Bad input: Error during negative model training. Minimum number of variants to use in training is larger than the whole call set. One can attempt to lower the --minNumBadVariants arugment but this is unsafe.**

I tried to lower this number, but different error message came up.

script used:

java -Xmx4g -jar GenomeAnalysisTK.jar -T VariantRecalibrator \
-mode BOTH -nt 4 \
-R hg19_all_MT.fasta \
-input \
-resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.fy_left.vcf \
-resourcemni,known=false,training=true,truth=false,prior=12.0 \
-resource:dbsnp,known=true,training=false,truth=false,prior=8.0 dbsnp137_sort_fy_left.vcf \
-recalFile \
-tranchesFile \
-rscriptFile \
-tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 -tranche 85.0 -tranche 80.0 \
-an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an MQ -an FS -an HRun 

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