expansionhunter

A tool for estimating large repeats in the bam.

Quick start

$ pbrun expansionhunter \
    --ref Ref/Homo_sapiens_assembly38.fasta \
    --in-bam input.bam \
    --in-variant-catalog catalogs/input/variants.json \
    --out-prefix output/repeats

expansionhunter Reference

Annotates existing BAM files with UMIs (Unique Molecular Indices) from a separate FASTQ file

Input/Output file options

--ref REF

Path to the Reference file. (default: None)

Option is required.

--in-bam IN_BAM

Path to the input BAM file. (default: None)

Option is required.

--in-variant-catalog IN_VARIANT_CATALOG

Path of input variant catalog file. (default: None)

Option is required.

--out-prefix OUT_PREFIX

Prefix for the output files. (default: None)

Option is required.

Options specific to this tool

--sex SEX

Specifies sex of the sample. It can be either female or male (default: female)

--region-extension-length REGION_EXTENSION_LENGTH

Specifies how far from on/off-target regions to search for informative reads. (default: 1000)

--analysis-mode ANALYSIS_MODE

Specify analysis mode, which can be either seeking or streaming. (default: seeking)

--num-threads NUM_THREADS

Specifies how many threads to can be used accelerate analysis of large variant catalogs. (default: 16)

Common options:

--logfile LOGFILE

Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)

--tmp-dir TMP_DIR

Full path to the directory where temporary files will be stored.

--with-petagene-dir WITH_PETAGENE_DIR

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)

--keep-tmp

Do not delete the directory storing temporary files after completion.

--license-file LICENSE_FILE

Path to license file license.bin if not in the installation directory.

--no-seccomp-override

Do not override seccomp options for docker (default: None).

--version

View compatible software versions.