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Badly formed genome location
I am trying to get depth of coverage using DepthOfCoverage tools of gatk for determining CNV. But I am consistently getting an error of badly formed genome location. Here is the command I am using for calculations:
java -Xmx3072m -jar GenomeAnalysisTK.jar -T DepthOfCoverage -nt 10 -I /home/MM_Data/cnv_data/group1.READS.bam.list -L /home/MM_Data/cnv_data/nexterarapidcapture_expandedexome_targetedregions.interval_list -R /home/refs/ucsc.hg19.fasta -dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 10 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 --includeRefNSites --countType COUNT_FRAGMENTS -o /home/MM_Data/cnv_data/group1.DATA
And the error statement is givine below:
##### ERROR MESSAGE: Badly formed genome location: Contig 'chr1 14362 14829' does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?
I am using the same reference ucsc hg19 fasta file which I used in whole pipeline for NGS processing and variant evaluation. I have downloaded the exome interval list from here as I was told to use exome interval for NXTR Rapid Cap Expand EXM kit Cat no. FC-140-1005. Gatk countLoci is working well with my bam files and gives number of loci. I don't know what I missed. Any suggestions........