A tool for estimating large repeats in the bam.
$ pbrun expansionhunter \
--ref Ref/Homo_sapiens_assembly38.fasta \
--in-bam input.bam \
--in-variant-catalog catalogs/input/variants.json \
--out-prefix output/repeats
Annotates existing BAM files with UMIs (Unique Molecular Indices) from a separate FASTQ file
Input/Output file options
- --ref REF
- --in-bam IN_BAM
- --in-variant-catalog IN_VARIANT_CATALOG
- --out-prefix OUT_PREFIX
Path to the Reference file. (default: None)
Option is required.
Path to the input BAM file. (default: None)
Option is required.
Path of input variant catalog file. (default: None)
Option is required.
Prefix for the output files. (default: None)
Option is required.
Options specific to this tool
- --sex SEX
- --region-extension-length REGION_EXTENSION_LENGTH
- --analysis-mode ANALYSIS_MODE
- --num-threads NUM_THREADS
Specifies sex of the sample. It can be either female or male (default: female)
Specifies how far from on/off-target regions to search for informative reads. (default: 1000)
Specify analysis mode, which can be either seeking or streaming. (default: seeking)
Specifies how many threads to can be used accelerate analysis of large variant catalogs. (default: 16)
Common options:
- --logfile LOGFILE
- --tmp-dir TMP_DIR
- --with-petagene-dir WITH_PETAGENE_DIR
- --keep-tmp
- --license-file LICENSE_FILE
- --no-seccomp-override
- --version
Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)
Full path to the directory where temporary files will be stored.
Full path to the PetaGene installation directory. By default, this should have been installed at /opt/petagene. Use of this option also requires that the PetaLink library has been preloaded by setting the LD_PRELOAD environment variable. Optionally set the PETASUITE_REFPATH and PGCLOUD_CREDPATH environment variables that are used for data and credentials (default: None)
Do not delete the directory storing temporary files after completion.
Path to license file license.bin if not in the installation directory.
Do not override seccomp options for docker (default: None).
View compatible software versions.