Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Docpatch #5047

Merged
merged 4 commits into from
Aug 28, 2018
Merged

Docpatch #5047

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
313496d
recommend --TMP-DIR
Jul 23, 2018
695e464
recommend --TMP-DIR
Jul 23, 2018
73f67ee
recommend --TMP-DIR
Jul 23, 2018
5facd13
edit docpatch
Aug 27, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 3 additions & 0 deletions src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
* </pre>
*
Expand All @@ -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
* </pre>
*
Expand All @@ -117,6 +119,7 @@
* <li>At least one interval must be provided</li>
* <li>Input GVCFs cannot contain multiple entries for a single genomic position</li>
* <li>The --genomicsdb-workspace-path must point to a non-existent or empty directory.</li>
* <li>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..</li>
* </ul>
*
* <h3>Developer Note</h3>
Expand Down
4 changes: 3 additions & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
* </pre>
*
* <h3>Caveats</h3>
Expand All @@ -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.</li>
* <li>Cannot take multiple GVCF files in one command.</li>
* <li>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.</li>
* </ul>
*
* <h3>Special note on ploidy</h3>
Expand Down