votebasedvcfmerger

Run votebasedvcfmerger to create union and intersection VCFs based on a minimum number of variant callers supporting a variant.

Earlier versions of Clara Parabricks referred to this as vbvm.

Quick Start

$ pbrun votebasedvcfmerger \
    --in-vcf firstfile:/absolute/path/to/input1.vcf \
    --in-vcf secondfile:/absolute/path/to/input2.vcf \
    --out-vcf output.vcf \
    --min-votes 3

votebasedvcfmerger Reference

Run votebasedvcfmerger to create union and intersection VCFs based on a minimum number of variant callers supporting a variant.

Input/Output file options

--in-vcf IN_VCF

A tag and VCF in the format <tag>:<vcf-file> where tag can be the name of the variant caller. The VCF file must be an absolute path. This option can be used multiple times, but at least two input VCFs are required. (default: None)

Option is required.

--out-dir OUT_DIR

Path for the directory where output VCF files will be created. Two VCFs unionVCF.vcf and filteredVCF.vcf will be saved at this location. (default: None)

Option is required.

Options specific to this tool

--min-votes MIN_VOTES

Minimum number of votes to consider for filtering the VCF. (default: None)

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.