diff --git a/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java b/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java index 3e0c8586f47..aa83957a8fb 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java @@ -86,6 +86,7 @@ * -V data/gvcfs/father.g.vcf.gz \ * -V data/gvcfs/son.g.vcf.gz \ * --genomicsdb-workspace-path my_database \ + * --tmp-dir=/path/to/large/tmp \ * -L 20 * * @@ -98,6 +99,7 @@ * --batch-size 50 \ * -L chr1:1000-10000 \ * --sample-name-map cohort.sample_map \ + * --tmp-dir=/path/to/large/tmp \ * --reader-threads 5 * * @@ -117,6 +119,7 @@ *
  • At least one interval must be provided
  • *
  • Input GVCFs cannot contain multiple entries for a single genomic position
  • *
  • The --genomicsdb-workspace-path must point to a non-existent or empty directory.
  • + *
  • GenomicsDBImport uses temporary disk storage during import. The amount of temporary disk storage required can exceed the space available, especially when specifying a large number of intervals. The command line argument `--tmp-dir` can be used to specify an alternate temporary storage location with sufficient space..
  • * * *

    Developer Note

    diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java index bf57138d2a0..d26b555586e 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java @@ -61,7 +61,8 @@ * gatk --java-options "-Xmx4g" GenotypeGVCFs \ * -R Homo_sapiens_assembly38.fasta \ * -V gendb://my_database \ - * -O output.vcf.gz + * -O output.vcf.gz \ + * --tmp-dir=/path/to/large/tmp * * *

    Caveats

    @@ -70,6 +71,7 @@ * programs produce files that they call GVCFs but those lack some important information (accurate genotype likelihoods * for every position) that GenotypeGVCFs requires for its operation. *
  • Cannot take multiple GVCF files in one command.
  • + *
  • The amount of temporary disk storage required by GenomicsDBImport may exceed what is available in the default location: `/tmp`. The command line argument `--tmp-dir` can be used to specify an alternate temperary storage location with sufficient space.
  • * * *

    Special note on ploidy