muse¶
Call somatic variants with the accelerated MuSE variant caller.
Quick Start¶
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
Compatible CPU Command¶
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
muse Reference¶
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 the 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)
Tool Option:¶
- --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 the VCF. Please see the 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.