Call somatic variants with the accelerated MuSE variant caller.
The following runs MuSE in call mode:
$ pbrun muse \
--mode call \
--ref Ref/Homo_sapiens_assembly38.fasta \
--in-tumor-bam tumor.bam \
--in-normal-bam normal.bam \
--out-vcf out.vcf
pbrun muse will append .MuSE.txt to the end of the file name provided in
--out-file.
The following runs MuSE in sump mode:
$ pbrun muse \
--mode sump \
--in-callfile muse_call_results.txt \
--out-vcf muse_sump_results.vcf \
--datatype G \
--in-dbsnp input.dbsnp.vcf.gz
The command below is the original CPU counterpart of the Parabricks commands 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.
./MuSE call -f Ref/Homo_sapiens_assembly38.fasta -O out.vcf tumor.bam normal.bam
Call variants with accelerated Muse variant caller
Input/Output file options
- --in-tumor-bam IN_TUMOR_BAM
-
Path to the input tumor bam file. (default: None)
- --in-normal-bam IN_NORMAL_BAM
-
Path to the input normal bam file. (default: None)
- --ref REF
-
Path to the input reference file. (default: None)
- --in-dbsnp IN_DBSNP
-
Path to the dbSNP vcf file that should be bgzip compressed, tabix indexed and based on the same reference genome used in call mode. (default: None)
- --in-callfile IN_CALLFILE
-
Path to the output file of muse call command. (default: None)
- --out-file OUT_FILE
-
Output stats file, .MuSE.txt will be automatically appended to this filename. (default: None)
- --out-vcf OUT_VCF
-
Output vcf file. (default: None)
Options specific to this tool
- --datatype DATATYPE
-
sample-specific error model to use. It can be either E (for whole exomes) or G (for whole genomes) (default: None)
- --mode MODE
-
Mode can be call or sump. User should first run muse with call mode and then run with sump mode to generate vcf. Please see MuSE somatic caller documentation for details. (default: None)
Option is required.
- --num-threads NUM_THREADS
-
Number of threads to run. Use 32 threads for maximum performance if your system has enough CPU threads. (default: 12)
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.