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Tranches plot issue
I think that this question has been asked before but I cannot find the way to fix the problem. I have just run VariantRecalibrator tool, and I'm getting this (see attached file) tranches plot for SNPs. I have understood correctly the tranches plot of the best practices manual but, I don't know what is going on here. I know that the tranches are sorted by Ti/Tv but for my, this plot makes no sense.
This is my command:
java -Xmx4g -jar GenomeAnalysisTK.jar \
-T VariantRecalibrator -R human_g1k_v37.fasta \
-input all.joinGeno.raw.vcf \
-resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.vcf \
-resource:omni,known=false,training=true,truth=true,prior=12.0 1000G_omni2.5.b37.vcf \
-resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.b37.vcf \
-resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.b37.vcf \
-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -mode SNP \
-tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 \
-recalFile recalibrate_SNP.recal \
-tranchesFile recalibrate_SNP.tranches \
Any help would be appreciated.