Variant Recalibrator Error: Track Input out of Coordinate Order on contig ....

Hi:

After running haplotypecaller on SNPs and Indels, I wanted to recalibrate the variant scores using VariantRecalibrator on SNPs and INDels simultaneously. Only 4 samples were used (just testing the pipeline right now). I am getting the following error saying one of the track inputs is out of coordinate order. Has anyone encountered a similar error?

ERROR ------------------------------------------------------------------------------------------

ERROR A USER ERROR has occurred (version 2.4-7-g5e89f01):

ERROR The invalid arguments or inputs must be corrected before the GATK can proceed

ERROR Please do not post this error to the GATK forum

ERROR

ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.

ERROR Visit our website and forum for extensive documentation and answers to

ERROR commonly asked questions http://www.broadinstitute.org/gatk

ERROR

ERROR MESSAGE: LocationAwareSeekableRODIterator: track input is out of coordinate order on contig chr4:140811083-140811084 compared to chr4:140811085

ERROR ------------------------------------------------------------------------------------------

[1]+ Exit 1 java -Xmx4g -jar $gatk -T VariantRecalibrator -R $ref2 -input ${data}/TruSeq/truseq.reduced.snps.indels.vcf --maxGaussians 6 -resource:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 $hapmap -resource:omni,VCF,known=false,training=true,truth=false,prior=12.0 $omni -resource:mills,VCF,known=true,training=true,truth=true,prior=12.0 $goldstandard -resource:dbsnp,VCF,known=true,training=false,truth=false,prior=6.0 $dbsnp -an QD -an MQRankSum -an ReadPosRankSum -an FS -an MQ -an ClippingRankSum -mode BOTH -recalFile ${data}/TruSeq/truseq.interstroke.snps.indels.reduced.recal -tranchesFile ${data}/TruSeq/truseq.interstroke.snps.indels.reduced.tranches -rscriptFile ${data}/TruSeq/truseq.interstroke.snps.indels.reduced.recal.plots.R

Thanks,

MC