glnexus
Scalable gVCF merging and joint variant calling for population sequencing projects (Original GLNexus Project).
$ pbrun glnexus \
--in-gvcf 1.gvcf \
--in-gvcf 2.gvcf \
--in-gvcf 3.gvcf \
--out-bcf out.bcf
Merge and joint-call input gVCF files, emitting multi-sample BCF.
Input/Output file options
- --in-gvcf IN_GVCF
- --bed BED
- --out-bcf OUT_BCF
Path to g.vcf or g.vcf.gz file. Option can be used multiple times. (default: None)
Option is required.
Three-column BED file with ranges to analyze (if neither --range nor --bed: use full length of all contigs). (default: None)
Path to output BCF file. (default: None)
Option is required.
Options specific to this tool
- --glnexus-options GLNEXUS_OPTIONS
- --dir DIR
Pass supported GLnexus options as one string. e.g. --glnexus-options="--list --squeeze". (default: None)
Scratch directory path (mustn't already exist; default: ./GLnexus.DB). (default: None)
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.