Denovo PIPELINE

Run the de novo mutation pipeline with 3 samples for de novo variant detection

../_images/denovo.png

Quick Start

CLI

# The commandline below will run Denovo pipeline.
$ pbrun denovomutation --ref Ref/Homo_sapiens_assembly38.fasta \
                --in-mother-bam mother.bam \
                --in-father-bam father.bam \
                --in-child-bam  child.bam \
                --out-prefix output

Options

--ref

Path to the reference file (default: None)

--in-bams

Paths to the three input BAM/CRAM files for variant calling. Order should be father, mother, and child. Each input file will be run through haplotypecaller and deepvariant (default: None)

--in-mother-bam

Paths to the input BAM/CRAM files for mother (default: None)

--in-father-bam

Paths to the input BAM/CRAM files for father (default: None)

--in-child-bam

Paths to the input BAM/CRAM files for child (default: None)

--out-prefix

Prefix filename for output data (default: None)

--disable-deepvariant

Generate results for haplotypecaller only (default: None)

--disable-haplotypecaller

Generate results for deepvariant only (default: None)

--pb-model-file

Path of non-default parabricks model file for deepvariant (default: None)

--disable-use-window-selector-model

Change the window selector model from Allele Count Linear to Variant Reads. This option will increase the accuracy and runtime (default: None)

--haplotypecaller-options

Pass supported haplotype caller options as one string. Currently supported original haplotypecaller options: -min-pruning <int>, -standard-min-confidence-threshold-for-calling <int>, -max-reads-per-alignment-start <int>, -min-dangling-branch-length <int>, -pcr-indel-model <NONE, HOSTILE, AGGRESSIVE, CONSERVATIVE>. e.g. –haplotypecaller-options=”-min-pruning 4 -standard-min-confidence-threshold-for-calling 30” (default: None)

--static-quantized-quals

Use static quantized quality scores to a given number of levels. Repeat this option multiple times for multiple bins (default: None)

--disable-read-filter

Disable the read filters for bam entries. Currently supported read filters that can be disabled: MappingQualityAvailableReadFilter, MappingQualityReadFilter, NotSecondaryAlignmentReadFilter, WellformedReadFilter (default: None)

--max-alternate-alleles

Maximum number of alternate alleles to genotype (default: None)

-G, --annotation-group

Which groups of annotations to add to the output variant calls. Currently supported annotation groups: StandardAnnotation, StandardHCAnnotation, AS_StandardAnnotation (default: None)

-GQB, --gvcf-gq-bands

Exclusive upper bounds for reference confidence GQ bands. Must be in the range [1, 100] and specified in increasing order (default: None)

--rna

Run haplotypecaller optimized for RNA Data (default: None)

--dont-use-soft-clipped-bases

Dont use soft clipped bases for variant calling (default: None)

--ploidy

Ploidy assumed for the bam file. Currently only haploid (ploidy 1) and diploid (ploidy 2) are supported (default: 2)

--dont-use-soft-clipped-bases

Dont use soft clipped bases for variant calling.

--ploidy PLOIDY

Ploidy assumed for the bam file. Currently only haploid (ploidy 1) and diploid (ploidy 2) are supported (default: 2)

--num-gpus NUM_GPUS

Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used. If you are using flexera, please include –gpu-devices too.

--gpu-devices GPU_DEVICES

Which 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.

--tmp-dir TMP_DIR

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

--no-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.