samtoolsmpileup

Accelerated mpileup functionality from samtools.

Quick Start

$ pbrun samtoolsmpileup \
    --in-bam wgs.bam \
    --out-file pileup.txt

Compatible SAMTools Command

The command below is the samtools counterpart of the Parabricks command above. The output from this command will be identical to the output from the above command.

samtools mpileup /w/wgs.bam -o pileup.txt -d 0

samtoolsmpileup Reference

Generate text pileup for one or multiple BAM files.

Input/Output file options

--ref REF

Path to the reference file. (default: None)

--in-bam IN_BAM

Path to the BAM/CRAM file. This option can be used multiple times. (default: None)

Option is required.

--out-file OUT_FILE

Path of output text pileup. If this option is not used, it will write to standard output. (default: None)

--interval-file INTERVAL_FILE

Path to a BED file (.bed) for selective access. This option can be used multiple times. (default: None)

Options specific to this tool

--num-threads NUM_THREADS

Number of threads for worker. (default: 12)

--min-mapq MIN_MAPQ

Skip alignments with mapping quality smaller than this value. (default: 0)

--enable-baq

Enable BAQ (per-Base Alignment Quality). (default: None)

-L INTERVAL, --interval INTERVAL

Interval within which to call the variants from the BAM file. Interval files should be passed using the --interval-file option. This option can be used multiple times. e.g. "-L chr1 -L chr2:10000 -L chr3:20000+ -L chr4:10000-20000". (default: None)

--anomalous-reads

Do not discard anomalous read pairs. (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.