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GenomeLocParser are incorrect: genome loc coordinates - exceed the contig size
Dear GATK team,
I am new to this forum and am tyring your tools for variant detection on human whole exome (Illumina)0 data.
I am using ucsc.hg19.fasta from your bundle as my reference. I am trying to use SelectVariants
to detect mutations in my annotated.vcf file (this file is the result of using HaplotypeCaller, followed by variant recalibration methods, functional annotation (using snpEff), and your VariantAnnotator tool). I am getting the following error that seems related to one of the intervals I am using (please see my command below my questions).
MESSAGE: Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The genome loc coordinates 140453100-140453140 exceed the contig size (133851895)
- Is this telling me that this particular interval is not represented in my annotated.vcf file (I have checked this file and don't find coordinates within this range)?
- If so, is there some way to subvert this error so that I only get output for those that are found?
java -Xmx2g -jar GenomeAnalysisTK.jar -T SelectVariants -R ucsc.hg19.fasta --variant annotated.vcf -o outputSV2.vcf -L my.interval_list
Thanks in advance.