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

(required) The reference file in fasta format.

--in-gvcf

(required) Path to g.vcf or g.vcf.gz file. Option can be used 2 or 3 times.

--out-variants

(required) Path to output merged g.vcf file.

--tmp-dir TMP_DIR

Full path to the directory where temporary files will be stored.

--seccomp-override

Do not override seccomp options for docker

--with-petagene-dir WITH_PETAGENE_DIR

Full path to the PetaGene installation directory where bin/ and species/ folders are located.

--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 installation directory.

--version

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

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

--dir

Scratch directory path (mustn’t already exist; default: ./GLnexus.DB) (default: None)

--bed

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

--out-bcf

Path to output BCF file (default: None)

--glnexus-options

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

--tmp-dir TMP_DIR

Full path to the directory where temporary files will be stored.

--seccomp-override

Do not override seccomp options for docker

--with-petagene-dir WITH_PETAGENE_DIR

Full path to the PetaGene installation directory where bin/ and species/ folders are located.

--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 installation directory.

--version

View compatible software versions.