GATK - doesn't see files

[Kath]

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

[nilshomer]

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

You are specifying the flags wrong. GATK wants the flags specified by "R=/PATH/hg19.fa D=/PATH/00-All.vcf" etc.

[Kath]

Thanks for your response. I tried using "R=" etc. but now it is saying "invalid argument value" for every argument.

Kath

[nilshomer]

Try this website: http://getsatisfaction.com/gsa