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VQSR question

Dear GATK team

I called SNPs using UG, followed by VQSR correction with GATK2.3-9. When I looked into the trenches.pdf file, I found the plot doesn't seem great (attached). It is WGS snp calls for 2 samples, and you can see the ti/tv is all the way below 2. However, I previously used the GATK 1.6.5 on the same dataset, giving ti/tv always around 2.09-2.12.

The resources used for VQSR correction is below - could you please take a look at the plot and see if it is normal? Thanks!

-resource:hapmap,known=false,training=true,truth=true,prior=15.0 $hapmap \
-resource:omni,known=false,training=true,truth=false,prior=12.0 $omni \
-resource:dbsnp,known=true,training=false,truth=false,prior=6.0 $dbsnp137 \
-an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an MQ -an DP \
-recalFile refinedSNP.recal \
-tranchesFile refinedSNP.tranches \
-rscriptFile refinedSNP.plots.R \
-mode SNP

Answers

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