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Syntax problem with VariantRecalibrator

jphekmanjphekman Broad InstituteMember

Running VariantRecalibrator on GATK (I know it's an older version - I need this version due to issues in more recent versions with functionality at a different step in my pipeline from this one. Also, I have tested this step on and get the same error.)

My command line:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx10G -jar /seq/vgb/software/gatk/gatk- VariantRecalibrator -R /seq/references/Canis_lupus_familiaris_assembly3/v1/Canis_lupus_familiaris_assembly3.fasta -V /seq/vgb/jphekman/singleBamToVcf/31001701034247.vcf --resource dbsnp,known=true,training=false,truth=false,prior=2.0:/seq/vgb/references/dog/population_variation/dog_dbSNP.vcf.gz -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an InbreedingCoeff -mode SNP -O /seq/vgb/jphekman/singleBamToVcf/31001701034247.recal --tranches-file /seq/vgb/jphekman/singleBamToVcf/31001701034247.tranches --rscript-file /seq/vgb/jphekman/singleBamToVcf/31001701034247.plots.R

The error:

A USER ERROR has occurred: Couldn't read file file:///home/unix/jphekman/dbsnp,known=true,training=false,truth=false,prior=2.0:/seq/vgb/references/dog/population_variation/dog_dbSNP.vcf.gz. Error was: It doesn't exist.

Note that both /seq/vgb/references/dog/population_variation/dog_dbSNP.vcf.gz and /seq/vgb/references/dog/population_variation/dog_dbSNP.vcf.gz.tbi do exist.

I've seen this error previously when I was using incorrect syntax in the --resources parameter. However I have perused the doc and I can't see where I'm going wrong. (Apologies if I'm missing something obvious.)


Help - what am I missing?


Best Answers


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