The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at

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

mesnaolamesnaola Member Posts: 1

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 Administrator, Dev Posts: 11,127 admin

    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.

    Geraldine Van der Auwera, PhD

Sign In or Register to comment.