Generate a summary file using samtoolsmpileup, which can be used for plotting/report
generation. You need to pass --extra-tools to the installer to use this tool.
$ pbrun vcfqcbybam \
--in-vcf sample.vcf \
--in-bam sample.bam \
--out-file output_pileup.txt\
--output-dir sample_qc
Generate a summary file using samtoolsmpileup that can be used for plotting/report generation.
Input/Output file options
- --ref REF
- --in-vcf IN_VCF
- --in-bam IN_BAM
- --out-file OUT_FILE
- --output-dir OUTPUT_DIR
- --interval-file INTERVAL_FILE
Path to the reference file. (default: None)
Path to the VCF file to be QC'ed. (default: None)
Option is required.
Path to the BAM file. This option can be used multiple times. (default: None)
Option is required.
Path of the output text pileup. (default: None)
Option is required.
Path to the directory that will contain all of the generated files. (default: None)
Option is required.
Path to a BED file for selective access. This option can be used multiple times. (default: None)
Tool Options:
- --num-threads NUM_THREADS
- --min-mapq MIN_MAPQ
- --enable-baq
- -L INTERVAL, --interval INTERVAL
- --anomalous-reads
- --output-mq
- --output-bp
- --window-size WINDOW_SIZE
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 mapping quality. (default: None)
Output base positions on reads. (default: None)
Size of the output plot window. (default: 1000)
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.