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.
$ pbrun vcfqc \
--in-vcf sample.vcf \
--output-dir sample_charts
Run vcfqc to generate QC plots on a VCF file.
Input/Output file options
- --in-vcf IN_VCF
- --output-dir OUTPUT_DIR
- --in-bamqc-dir IN_BAMQC_DIR
Path to the VCF file. (default: None)
Option is required.
Output Directory to store all images. (default: None)
Option is required.
Input directory containing BAMQC images. These should be the output of collectmultiplemetrics. (default: None)
Tool Options:
- --allele-depth ALLELE_DEPTH
- --depth DEPTH
- --map-quality MAP_QUALITY
- --genotype-quality GENOTYPE_QUALITY
- --vaf VAF
- --window-size WINDOW_SIZE
- --image-format IMAGE_FORMAT
allele-depth column to be QC'ed. (default: None)
Depth column to be QC'ed. (default: None)
Mapping Quality column to be QC'ed. (default: None)
Genotype Quality to be QC'ed (default: None)
Variant Allele Frequency to be QC'ed. (default: None)
Window size for the vcfqc tool. (default: 1000)
Image format for saved plots [png]. (default: png)
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.
GPU options:
- --num-gpus NUM_GPUS
- --gpu-devices GPU_DEVICES
Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used.
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.