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.
$ pbrun manta \
--ref Ref/Homo_sapiens_assembly38.fasta \
--in-tumor-bam tumor.bam \
--in-normal-bam normal.bam \
--out-prefix output
Analyze germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
Input/Output file options
- --ref REF
- --in-tumor-bam IN_TUMOR_BAM
- --in-normal-bam IN_NORMAL_BAM
- --bed BED
- --out-prefix OUT_PREFIX
Path to the reference file. (default: None)
Option is required.
Path of BAM file for tumor reads. (default: None)
Path of BAM file for normal reads. This option can be used multiple times. (default: None)
Optional bgzip-compressed/tabix-indexed BED file containing the set of regions to call. (default: None)
Prefix filename for output data. (default: None)
Option is required.
Options specific to this tool
- --num-threads NUM_THREADS
- --manta-options MANTA_OPTIONS
Number of threads for worker. (default: 1)
Pass supported manta options as one string. e.g. --manta-options="--rna --unstrandedRNA". (default: None)
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.