The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

#### ☞ Did you remember to?

1. Search using the upper-right search box, e.g. using the error message.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

#### ☞ Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ` ) each to make a code block as demonstrated here.

GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

# Training data for VariantRecalibrator (Mouse)

Posts: 4
edited January 2013

Dear all,

I was calling SNP from Mouse samples using GATK and was in the step of "Variant quality score recalibration". The VariantRecalibrator walker asked me to provide training sets for mouse SNPs. The only SNP data (for the USCS mm9 assembly) I can find right now is the dbSNP. So I tried the run VariantRecalibrator like this:

java -Xmx4g -jar GenomeAnalysisTK.jar
-T VariantRecalibrator
-R Refseq.fa
-input snps.raw.vcf
-resource:dbsnp,known=true,training=false,truth=false,prior=6.0 snp128.vcf
-an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an MQ -an InbreedingCoeff
-mode BOTH
-recalFile output.recal
-tranchesFile output.tranches
-rscriptFile output.plots.R

However, the program asked for more:

##### ERROR ------------------------------------------------------------------------------------------

I was wondering if I can change the parameters by setting both the training/truth to true:

-resource:dbsnp,known=true,training=true,truth=true,prior=6.0 snp128.vcf

or should I ignore the "-resource" option at the cost of being less accurate?

Any suggestions would be greatly appreciated.

Thanks!

Tuo

Post edited by Geraldine_VdAuwera on
Tagged:

• Posts: 122 ✭✭✭

Hi there,

Yeah, the text of the user exception error message is telling you that it needs some set of sites to use as a training set. You can indicate this by marking one of the resources as training=true

Your proposed parameters make a lot of sense if that is the only database of variants that you have for your organism.

I hope that helps,

• Posts: 94

I got this error when using the VariantRecalibrator:

##### 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.

What shoild I do?