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.

Quick Start

$ pbrun vcfqcbybam \
    --in-vcf sample.vcf \
    --in-bam sample.bam \
    --out-file output_pileup.txt\
    --output-dir sample_qc

vcfqcbybam Reference

Generate a summaryfile using samtoolsmpileup that can be used for plotting/report generation.

Input/Output file options

--ref REF

Path to the reference file. (default: None)

--in-vcf IN_VCF

Path to the VCF file to be QC'ed. (default: None)

Option is required.

--in-bam IN_BAM

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

Option is required.

--out-file OUT_FILE

Path of output text pileup. (default: None)

Option is required.

--output-dir OUTPUT_DIR

Path to the directory that will contain all of the generated files. (default: None)

Option is required.

--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 (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)

--window-size WINDOW_SIZE

Size of output plot window. (default: 1000)

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)


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.


Do not override seccomp options for docker (default: None).


View compatible software versions.