The variant quality score recalibrator builds an adaptive error model using known variant sites and then applies this model to estimate the probability that each variant is a true genetic variant or a machine artifact. VQSR must be run twice in succession in order to build a separate error model for SNPs and INDELs. One major improvement from previous recommended protocols is that hand filters do not need to be applied at any point in the process now. All filtering criteria are learned from the data itself.
java -Xmx4g -jar GenomeAnalysisTK.jar \ -T VariantRecalibrator \ -R path/to/reference/human_g1k_v37.fasta \ -input raw.input.vcf \ -recalFile path/to/output.recal \ -tranchesFile path/to/output.tranches \ -nt 4 \ [SPECIFY TRUTH AND TRAINING SETS] \ [SPECIFY WHICH ANNOTATIONS TO USE IN MODELING] \ [SPECIFY WHICH CLASS OF VARIATION TO MODEL] \
For SNPs we use both HapMap v3.3 and the Omni chip array from the 1000 Genomes Project as training data. In addition we take the highest confidence SNPs from the project's callset. These datasets are available in the GATK resource bundle. Arguments for VariantRecalibrator command:
-percentBad 0.01 -minNumBad 1000 \ -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf \ -resource:omni,known=false,training=true,truth=true,prior=12.0 1000G_omni2.5.b37.sites.vcf \ -resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.vcf \ -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp.b37.vcf \ -an QD -an MQRankSum -an ReadPosRankSum -an FS -an DP \ -mode SNP \
Note that, for the above to work, the input vcf needs to be annotated with the corresponding values (QD, FS, DP, etc.). If any of these values are somehow missing, then VariantAnnotator needs to be run first so that VariantRecalibration can run properly.
Also, using the provided sites-only truth data files is important here as parsing the genotypes for VCF files with many samples increases the runtime of the tool significantly.
Some of these annotations might not be the best for your particular dataset. For example, InbreedingCoeff is a population level statistic that requires at least 10 samples in order to be calculated. If your study design has more than 10 samples then it is recommended to be included.
Depth of coverage (the DP annotation invoked by Coverage) should not be used when working with hybrid capture datasets since there is extreme variation in the depth to which targets are captured! In whole genome experiments this variation is indicative of error but that is not the case in capture experiments.
Additionally, the UnifiedGenotyper produces a statistic called the HaplotypeScore which should be used for SNPs. This statistic isn't necessary for the HaplotypeCaller because that mathematics is already built into the likelihood function itself when calling full haplotypes.
In our testing we've found that in order to achieve the best exome results one needs to use an exome SNP and/or indel callset with at least 30 samples. For users with experiments containing fewer exome samples there are several options to explore:
When modeling indels with the VQSR we use a training dataset that was created at the Broad by strictly curating the (Mills, Devine, Genome Research, 2011) dataset as as well as adding in very high confidence indels from the 1000 Genomes Project. This dataset is available in the GATK resource bundle. Arguments for VariantRecalibrator:
--maxGaussians 4 -percentBad 0.01 -minNumBad 1000 \ -resource:mills,known=false,training=true,truth=true,prior=12.0 Mills_and_1000G_gold_standard.indels.b37.sites.vcf \ -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp.b37.vcf \ -an DP -an FS -an ReadPosRankSum -an MQRankSum \ -mode INDEL \
Note that indels use a different set of annotations than SNPs. Most annotations related to mapping quality have been removed since there is a conflation with the length of an indel in a read and the degradation in mapping quality that is assigned to the read by the aligner. This covariation is not necessarily indicative of being an error in the same way that it is for SNPs.
InbreedingCoeff is a population level statistic that requires at least 10 samples in order to be calculated. If your study design has more than 10 samples then it is recommended to be included.
The power of the VQSR is that it assigns a calibrated probability to every putative mutation in the callset. The user is then able to decide at what point on the theoretical ROC curve their project wants to live. Some projects, for example, are interested in finding every possible mutation and can tolerate a higher false positive rate. On the other hand, some projects want to generate a ranked list of mutations that they are very certain are real and well supported by the underlying data. The VQSR provides the necessary statistical machinery to effectively apply this sensitivity/specificity tradeoff.
java -Xmx3g -jar GenomeAnalysisTK.jar \ -T ApplyRecalibration \ -R reference/human_g1k_v37.fasta \ -input raw.input.vcf \ -tranchesFile path/to/input.tranches \ -recalFile path/to/input.recal \ -o path/to/output.recalibrated.filtered.vcf \ [SPECIFY THE DESIRED LEVEL OF SENSITIVITY TO TRUTH SITES] \ [SPECIFY WHICH CLASS OF VARIATION WAS MODELED] \
For SNPs we used HapMap 3.3 and the Omni 2.5M chip as our truth set. The default recommendation is to achieve 99.9% sensitivity to the accessible truth sites. Naturally projects involving a higher degree of diversity in terms of world populations can expect to achieve a higher truth sensitivity.
--ts_filter_level 99.9 \ -mode SNP \
For indels we use the Mills / 1000 Genomes indel truth set described above. The default recommendation is to achieve 99.9% sensitivity to the accessible truth sites. Naturally projects involving a higher degree of diversity in terms of world populations can expect to achieve a higher truth sensitivity.
--ts_filter_level 99.9 \ -mode INDEL \
