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Error in DepthOfCoverage for interval of 1bp

I'm getting an error while running DepthOfCoverage (GATK v2014.3-3.2.2-7-gf9cba99) to find coverage information for human whole-exome using the BAM file (sorted, indel-realigned, base-recalibrated) against specific intervals with varying sizes ranging from 1bp to hundreds. I'm encountering the following error message by GATK:

ERROR MESSAGE: File associated with name GRch37_intervals.bed is malformed: Problem reading the interval file caused by Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The stop position 153789008 is less than start 153789009 in contig 5

Snippet of my interval file :
5 153783664 153783771 int11
5 153789008 153789008 int12
5 153789101 153789322 int13

I don't want to eliminate intervals with single nucleotide.

Best Answer


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