vcfqc

Generates QC charts from the input VCF. You need to pass --extra-tools to the installer to use this tool. This tool supports single sample VCFs only.

Quick Start

$ pbrun vcfqc \
    --in-vcf sample.vcf \
    --output-dir sample_charts

vcfqc Reference

Run vcfqc to generate QC plots on a VCF file.

Input/Output file options

--in-vcf IN_VCF

Path to the VCF file. (default: None)

Option is required.

--output-dir OUTPUT_DIR

Output Directory to store all images. (default: None)

Option is required.

--in-bamqc-dir IN_BAMQC_DIR

Input directory containing BAMQC images. These should be the output of collectmultiplemetrics. (default: None)

Options specific to this tool

--allele-depth ALLELE_DEPTH

allele-depth column to be QC'ed. (default: None)

--depth DEPTH

Depth column to be QC'ed. (default: None)

--map-quality MAP_QUALITY

Mapping Quality column to be QC'ed. (default: None)

--genotype-quality GENOTYPE_QUALITY

Genotype Quality to be QC'ed (default: None)

--vaf VAF

Variant Allele Frequency to be QC'ed. (default: None)

--window-size WINDOW_SIZE

Window size for the vcfqc tool. (default: 1000)

--image-format IMAGE_FORMAT

Image format for saved plots [png]. (default: png)

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.

GPU options:

--num-gpus NUM_GPUS

Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used.

--gpu-devices GPU_DEVICES

GPU devices to use for a run. By default, all GPU devices will be used. To use specific GPU devices, enter a comma-separated list of GPU device numbers. Possible device numbers can be found by examining the output of the nvidia-smi command. For example, using --gpu-devices 0,1 would only use the first two GPUs.