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Strange VQSR plots after version 3.5 release
I ran GATK's cohort genotyping pipeline on 5000 human samples with Illumina WGS ~1.3x data, up through GenotypeGVCFs (and CatVariants to combine chunks) using v3.4-46. Next I ran VariantRecalibrator (initially just chr1) using recommended settings with both v3.4-46 and v3.5. Here is my command for both versions:
java -Xmx40g \
-jar GenomeAnalysisTK.jar \
-T VariantRecalibrator \
-R hs37m.fa \
-input gatk.hc.combined.genotyped.chr1-22.vcf.gz \
-recalFile snps.recal \
-tranchesFile snps.tranches \
-rscriptFile recalibrate_SNP_plots.R \
--target_titv 2.15 \
-nt 24 \
-resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.vcf.gz \
-resource:omni,known=false,training=true,truth=true,prior=12.0 1000G_omni2.5.b37.vcf.gz \
-resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.b37.vcf.gz \
-resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.b37.vcf.gz \
-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an DP -an InbreedingCoeff \
-mode SNP \
-L 1 \
-tranche 100.0 -tranche 99.9 -tranche 99.5 -tranche 99.0 -tranche 98.5 -tranche 90.0 \
--maxGaussians 6 \
The attached tranches plots (snps.tranches.v3.5.pdf) generated w/ v3.5 look strange because:
1) The tranches are out of order on the bar plot (e.g., 99.5 is before 99)
2) The fill coloring doesn't make sense for tranches 99 and 98.5 - there are orange stripes over the blue bar
3) The scatter plot's connecting lines go in both directions
The plots for v3.4-46 look more normal (snps.tranches.v3.4-46.pdf), though I'm still trying to figure out how to get closer to the expected 2.15 Ti/Tv ratio. Oddly, the Ti/Tv ratios differ slightly between v3.4-46 and v3.5 even though the same data and settings were used.
I suspected the behavior w/ v3.5 may be a possible bug in VariantRecalibrator, which is why I'm posting here. Please let me know if you need any more information.