Scalable gVCF merging and joint variant calling for population sequencing projects (Original GLNexus Project).

Quick Start

$ pbrun glnexus \
    --in-gvcf 1.gvcf \
    --in-gvcf 2.gvcf \
    --in-gvcf 3.gvcf \
    --out-bcf out.bcf

glnexus Reference

Merge and joint-call input gVCF files, emitting multi-sample BCF.

Input/Output file options

--in-gvcf IN_GVCF

Path to g.vcf or g.vcf.gz file. Option can be used multiple times. (default: None)

Option is required.

--bed BED

Three-column BED file with ranges to analyze (if neither --range nor --bed: use full length of all contigs). (default: None)

--out-bcf OUT_BCF

Path to output BCF file. (default: None)

Option is required.

Options specific to this tool

--glnexus-options GLNEXUS_OPTIONS

Pass supported GLnexus options as one string. e.g. --glnexus-options="--list --squeeze". (default: None)

--dir DIR

Scratch directory path (mustn't already exist; default: ./GLnexus.DB). (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)


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).


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