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GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

Error wit BaseRecalibrator: The stop position ... is less than start ...

I am using GATK version 2.4.9. When trying to execute BaseRecalibrator I get this message:

ERROR MESSAGE: Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The stop position 4580 is less than start 4581 in contig chr1

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.



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Mikel,

    Keep in mind that the BED format is 0-based for the start coordinates, so coordinates taken from 1-based formats should be offset by 1. This may explain the error you're getting.

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