Hi,
I'm probably being really stupid but can anyone tell me why GATK is failing to load my reference dictionary. I have a folder containing the fasta files including the .fai, .dict etc. The command I am using is (where PATH is the path to the relevant folder):
$ java –Xmx4g –Djava.io.tmpdir=/local –jar /PATH/GenomeAnalysisTK-1.0.4418/GenomeAnalysisTK.jar –R /PATH/hg19.fa –D /PATH/00-All.vcf –I input.bam –T CountCovariates –cov ReadGroupCovariate –cov QualityScoreCovariate –cov DinucCovariate –cov CycleCovariate –recalFile table.recal_data.csv
Do I need to put all the reference files (.fai, .dict etc.) into the command?
Thanks
Kath
I'm probably being really stupid but can anyone tell me why GATK is failing to load my reference dictionary. I have a folder containing the fasta files including the .fai, .dict etc. The command I am using is (where PATH is the path to the relevant folder):
$ java –Xmx4g –Djava.io.tmpdir=/local –jar /PATH/GenomeAnalysisTK-1.0.4418/GenomeAnalysisTK.jar –R /PATH/hg19.fa –D /PATH/00-All.vcf –I input.bam –T CountCovariates –cov ReadGroupCovariate –cov QualityScoreCovariate –cov DinucCovariate –cov CycleCovariate –recalFile table.recal_data.csv
Do I need to put all the reference files (.fai, .dict etc.) into the command?
Thanks
Kath
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