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GATK4.1.0.0's VariantRecalibrator resource format differs from GATK4.0.11.0?

xiuczxiucz Member
edited March 2019 in Ask the GATK team

Hi,
When I used GATK4.1.0.0 to vqsr, I found it reported the error, but I tried the beta version GATK4.0.11.0, it ran well.
And the input VCF file I used was produced by the old tool CombineGVCFs and GenotypeGVCFs with gvcfs. I do not use GenomicsDBImport, because it is really slow for me.
gatk4.0.11.0

~/gatk-4.0.11.0/gatk --java-options '-Xmx20G -DGATK_STACKTRACE_ON_USER_EXCEPTION=true' VariantRecalibrator \
-R ~/database/hg19/ucsc.hg19.fasta \
-V ~/test.raw.vcf \
-resource hapmap,known=false,training=true,truth=true,prior=15.0:~/GATK_hg19/hapmap_3.3.hg19.sites.vcf \
-an QD -an FS -an SOR -an MQ -an MQRankSum -an ReadPosRankSum \
-mode SNP \
-tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 \
-O out/recalibrate_SNP.recal \
--tranches-file out/test.recalibrate_SNP.tranches \
--rscript-file out/test.recalibrate_SNP_plots.R

gatk4.1.0.0

~/gatk-4.0.11.0/gatk --java-options '-Xmx20G -DGATK_STACKTRACE_ON_USER_EXCEPTION=true' VariantRecalibrator \
-R ~/database/hg19/ucsc.hg19.fasta \
-V ~/test.raw.vcf \
-resource hapmap,known=false,training=true,truth=true,prior=15.0:~/GATK_hg19/hapmap_3.3.hg19.sites.vcf \
-an QD -an FS -an SOR -an MQ -an MQRankSum -an ReadPosRankSum \
-mode SNP \
-tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 \
-O out/recalibrate_SNP.recal \
--tranches-file out/test.recalibrate_SNP.tranches \
--rscript-file out/test.recalibrate_SNP_plots.R

Error:

A USER ERROR has occurred: Couldn't read file file:/// ./out/code/hapmap,known=false,training=true,truth=true,prior=15.0:~/GATK_hg19/hapmap_3.3.hg19.sites.vcf. Error was: It doesn't exist.

But the resource file really exists here. I don't know how to resolve it, or GATK4.1.0.0 dose not support the the old combine gvcfs way any longer?

Best Answer

Answers

  • xiuczxiucz Member

    I find another question, when I use GenomicsDBImport tool, it produces lots of json files in /tmp dir, causing a warning of "cannot create temp file for here-document: No space left on device". Can I specify some parameters to avoid the terrible problem ?

  • xiuczxiucz Member

    @AdelaideR thank you for your useful links, which really helped me. And for the second question, I run GATK on my local machine, I will try a docker later, thank you again.

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