bcftoolscall
Accelerated bcftools call. bcftoolscall calls variants from mpileup output.
$ pbrun bcftoolscall \
--in-file pileup.bcf \
--out-file output.vcf
The command below is the CPU counterpart of the Parabricks command above. The output from this command will be identical to the output from the above command. Please see the Output Comparison page for comparing the results.
bcftools call pileup.bcf -c -o output.vcf
Call variants from mpileup data.
Input/Output file options
- --in-file IN_FILE
- --out-file OUT_FILE
Path to the input mpileup file. (default: None)
Option is required.
Path of the output file. If this option is not used, it will write to standard output. (default: None)
Tool Options:
- --num-threads NUM_THREADS
- --variant-sites
Number of threads for worker. (default: 1)
Output variant sites only. (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.