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# NaN LOD in VQSR

Posts: 31Member

Hi all, I'm running VariantRecalibrator on a SNP set (47 exomes) and I get this error:

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.2-3-gde33222):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### 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)
##### ERROR ------------------------------------------------------------------------------------------


this is the command line:

    java -Djava.io.tmpdir=/lustre2/scratch/  -Xmx32g -jar /lustre1/tools/bin/GenomeAnalysisTK-2.2-3.jar \
-T VariantRecalibrator \
-R /lustre1/genomes/hg19/fa/hg19.fa \
-input /lustre1/workspace/Ferrari/Carrera/Analysis/UG/bpd_ug.SNP.vcf \
-resource:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 /lustre1/genomes/hg19/annotation/hapmap_3.3.hg19.sites.vcf.gz \
-resource:omni,VCF,known=false,training=true,truth=false,prior=12.0 /lustre1/genomes/hg19/annotation/1000G_omni2.5.hg19.sites.vcf.gz \
-resource:dbsnp,VCF,known=true,training=false,truth=false,prior=6.0 /lustre1/genomes/hg19/annotation/dbSNP-137.chr.vcf -an QD \
-an HaplotypeScore \
-an MQRankSum \
-an ReadPosRankSum \
-an FS \
-an MQ \
-an DP \
-an QD \
-an InbreedingCoeff \
-mode SNP \
-recalFile /lustre2/scratch/Carrera/Analysis2/snp.ug.recal.csv \
-tranchesFile /lustre2/scratch/Carrera/Analysis2/snp.ug.tranches \
-rscriptFile /lustre2/scratch/Carrera/Analysis2/snp.ug.plot.R \
-U ALLOW_SEQ_DICT_INCOMPATIBILITY \
--maxGaussians 6


I've already tried to decrease the --maxGaussians option to 4, I've also added --percentBad option (setting it up to 0.12, as for INDEL) but I still get the error. I've added the option -debug to see what's happening, but apparently this has been removed from GATK-2.2. Any help is appreciated... thanks

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## Best Answer

• Posts: 6,085 admin
Answer ✓

Hmm, that might be a bug in the error reporting, we'll check it out. Thanks for the update.

Geraldine Van der Auwera, PhD

## Answers

• Posts: 31Member

Apparently the error vanishes if I remove -an QD

• Posts: 122GATK Developer mod
edited November 2012

Hi there,

Can you please post the full log output from this run? There is some useful information in there about the annotation distributions, &c. that will help us narrow down any issues.

Cheers,

Post edited by rpoplin on
• Posts: 31Member

I realized that the first code had two entries for -an QD, which I believe was the cause of the whole thing...

• Posts: 6,085Administrator, GATK Developer admin

Good catch, I didn't notice that. We still need to fix the error handling though, since the program clearly isn't handling the problem correctly.

Geraldine Van der Auwera, PhD

• Posts: 37Member

This error also appears if you include some annotations with -an that VQSR doesn't like, e.g. I ran the command with lots of annotations, failed with the above error, re-ran with just -an BaseQRankSum -an DP -an FS -an HaplotypeScore -an MQ -an MQRankSum -an QD -an ReadPosRankSum = success.

• Posts: 6,085Administrator, GATK Developer admin

Hmm, can you be more specific about which annotations were involved in the failure?

Geraldine Van der Auwera, PhD

• Posts: 37Member

I stuck most of them in, so -an AC -an AF etc, it was a bit of a case of 'suck it and see' to get a better feel for the results, so probably not the ideal thing to do but it did give me the same error as above, cheers.

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