Im trying to use GATK DepthofCoverage, but Im getting an error which I do not understand how to resolve.
My command is:
But then I get:
##### ERROR MESSAGE: File associated with name ~/BED/exons.b37.bed is malformed: Interval file could not be parsed in any supported format. caused by BED files must be parsed through Tribble; parsing them as intervals through the GATK engine is no longer supported
##### ERROR ------------------------------------------------------------------------------------------
The GATK wiki does not have many examples of what can be used. This is Whole Exome sequencing data, so naturally I want to determine the coverage over all exon intervals.
I have no clue what this Tribble thing is, and how can they not support BED format....
Thanks.
My command is:
Code:
java -Xmx4g -jar ~/GenomeAnalysisTK-1.3/GenomeAnalysisTK.jar \ -T DepthOfCoverage \ -R ~/b37_genomes/human_g1k_v37.fasta \ -I PE.merged.sorted.recal.bam \ -L ~/BED/exons.b37.bed \ -o test.GATK.out
##### ERROR MESSAGE: File associated with name ~/BED/exons.b37.bed is malformed: Interval file could not be parsed in any supported format. caused by BED files must be parsed through Tribble; parsing them as intervals through the GATK engine is no longer supported
##### ERROR ------------------------------------------------------------------------------------------
The GATK wiki does not have many examples of what can be used. This is Whole Exome sequencing data, so naturally I want to determine the coverage over all exon intervals.
I have no clue what this Tribble thing is, and how can they not support BED format....
Thanks.
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