bcftoolsmpileup
Accelerated mpileup functionality from bcftools.
$ pbrun bcftoolsmpileup \
--in-bam wgs.bam \
--out-file pileup.vcf
The command below is the bcftools counterpart of the Parabricks command above. The output from this command will be identical to the output from the above command.
bcftools mpileup wgs.bam -o pileup.txt -d 2147483647
Generate BCF/VCF pileup for one or multiple BAM files.
Input/Output file options
- --ref REF
- --in-bam IN_BAM
- --out-file OUT_FILE
- --interval-file INTERVAL_FILE
Path to the reference file. This is not required if the --no-reference option is passed. (default: None)
Path to the BAM file. This option can be used multiple times. (default: None)
Option is required.
Path of output file. If this option is not used, it will write to standard output. By default, the output will be uncompressed VCF. To output uncompressed BCF, use the --bcf option. (default: None)
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
- --min-mapq MIN_MAPQ
- --enable-baq
- -L INTERVAL, --interval INTERVAL
- --anomalous-reads
- --bcf
- --no-reference
- --no-version
Number of threads for worker. (default: 12)
Skip alignments with mapping quality smaller than this value. (default: 0)
Enable BAQ (per-Base Alignment Quality). (default: None)
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)
Do not discard anomalous read pairs. (default: None)
Output uncompressed BCF. (default: None)
Do not require fasta reference file. (default: None)
Do not append version and command line to the header.
(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.