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 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.