bcftoolscall

Accelerated bcftools call. bcftoolscall calls variants from mpileup output.

Quick Start

$ pbrun bcftoolscall \
    --in-file pileup.bcf \
    --out-file output.vcf

Compatible CPU Command

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

bcftoolscall Reference

Call variants from mpileup data.

Input/Output file options

--in-file IN_FILE

Path to the input mpileup file. (default: None)

Option is required.

--out-file OUT_FILE

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

Number of threads for worker. (default: 1)

--variant-sites

Output variant sites only. (default: None)

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.