I am using GATK version 2.4.9. When trying to execute BaseRecalibrator I get this message:
I'm not specifying any of the advanced options, just an input BAM, the reference genome and a BED file for the -knownSites argument. The BAM file has been correctly validated with Picard and I've checked the BED and all stop positions are greater or equal to the start positions.
I also tried with an older version of GATK so that I could use CountCovariates, but it gave a similar error (same error with different start and stop positions).
The exact call to the method is:
java -Xmx4g -jar GenomeAnalysisTK.jar -T BaseRecalibrator -I XXXX.marked.realigned.fixed.bam -R hg18KO.fa -knownSites dbsnp130_hg18_KO.bed -o XXXX_recal_data.grp
Any help would be greatly appreciated.