smoove

Call and genotype SVs for short reads using smoove (Original Smoove Project). This tool is not accelerated, and the original precompiled binary will be run on the server.

Quick Start

$ pbrun smoove \
    --ref Ref/Homo_sapiens_assembly38.fasta \
    --in-bam  in.bam \
    --output-dir  output \
    --name  SM

Compatible CPU Command

The command below is the original CPU counterpart of the Parabricks command above. The output from this command will be identical to the output from the above command. See the Output Comparison page for comparing the results.

./smoove call --fasta Ref/Homo_sapiens_assembly38.fasta \
--outdir output \
--name SM \
in.bam

smoove Reference

Call and genotype SVs for short reads.

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/CRAM file for variant calling. (default: None)

Option is required.

--output-dir OUTPUT_DIR

Path to the directory that will contain all of the generated files. (default: None)

Option is required.

Options specific to this tool

--name NAME

Input sample name. (default: None)

Option is required.

--smoove-options SMOOVE_OPTIONS

Pass supported smoove options as one string. e.g. --smoove-options="--excludechroms chr4 --noextrafilters". (default: None)

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.