JOINT CALLING
NVIDIA Clara Parabricks Pipelines accelerated tools for joint calling
Combing 2 or 3 GVCF samples in a fast way
QUICK START
$ pbrun triocombinegvcf --ref Ref.fa --in-gvcf father.g.vcf \
--in-gvcf mother.g.vcf --in-gvcf child.g.vcf \
--out-variants combined.g.vcf
COMPATIBLE CPU GATK4 COMMAND
$ gatk CombineGVCFs -R Ref.fa -V father.g.vcf -V mother.g.vcf \
-V child.g.vcf -O combined.g.vcf
OPTIONS
- --ref
- --in-gvcf
- --out-variants
(required) The reference file in fasta format.
(required) Path to g.vcf or g.vcf.gz file. Option can be used 2 or 3 times.
(required) Path to output merged g.vcf file.
- --tmp-dir TMP_DIR
- --with-petagene-dir WITH_PETAGENE_DIR
- --keep-tmp
- --license-file LICENSE_FILE
- --version
Full path to the directory where temporary files will be stored.
Full path to the PetaGene installation directory where bin/ and species/ folders are located.
Do not delete the directory storing temporary files after completion.
Path to license file license.bin if not in installation directory.
View compatible software versions.
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
OPTIONS
- --in-gvcf
- --dir
- --bed
- --out-bcf
- --glnexus-options
Path to g.vcf or g.vcf.gz file. Option can be used multiple times (default: None)
Scratch directory path (mustn’t already exist; default: ./GLnexus.DB) (default: None)
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)
Pass supported GLnexus options as one string. e.g. –glnexus-options=”–list –squeeze” (default: None)
- --tmp-dir TMP_DIR
- --with-petagene-dir WITH_PETAGENE_DIR
- --keep-tmp
- --license-file LICENSE_FILE
- --version
Full path to the directory where temporary files will be stored.
Full path to the PetaGene installation directory where bin/ and species/ folders are located.
Do not delete the directory storing temporary files after completion.
Path to license file license.bin if not in installation directory.
View compatible software versions.