manta

Structural variant (SV) and indel caller from mapped paired-end sequencing reads. This tool is not accelerated and the original precompiled binary will be run on the server.

Quick Start

$ pbrun manta \
    --ref Ref/Homo_sapiens_assembly38.fasta \
    --in-tumor-bam tumor.bam \
    --in-normal-bam normal.bam \
    --out-prefix output

manta Reference

Analyze germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.

Input/Output file options

--ref REF

Path to the reference file. (default: None)

Option is required.

--in-tumor-bam IN_TUMOR_BAM

Path of BAM file for tumor reads. (default: None)

--in-normal-bam IN_NORMAL_BAM

Path of BAM file for normal reads. This option can be used multiple times. (default: None)

--bed BED

Optional bgzip-compressed/tabix-indexed BED file containing the set of regions to call. (default: None)

--out-prefix OUT_PREFIX

Prefix filename for output data. (default: None)

Option is required.

Options specific to this tool

--num-threads NUM_THREADS

Number of threads for worker. (default: 1)

--manta-options MANTA_OPTIONS

Pass supported manta options as one string. e.g. --manta-options="--rna --unstrandedRNA". (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.