denovomutation - NVIDIA Docs

NVIDIA Docs Hub NVIDIA Clara Clara Parabricks v3.7.0 denovomutation

Run the de novo mutation pipeline with three samples for de novo variant detection.

Quick Start

The following command runs the de novo pipeline.

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            $ 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

denovomutation Reference

(BETA) Run the de novo mutation pipeline with 3 samples for de novo variant detection.

Input/Output file options

--ref REF

Path to the reference file. (default: None)

Option is required.

--in-father-bam IN_FATHER_BAM

Path to the input BAM/CRAM file of father for variant calling. This input file will be run through haplotypecaller and deepvariant. (default: None)

Option is required.

--in-mother-bam IN_MOTHER_BAM

Path to the input BAM/CRAM file of mother for variant calling. This input file will be run through haplotypecaller and deepvariant. (default: None)

Option is required.

--in-child-bam IN_CHILD_BAM

Path to the input BAM/CRAM file of child for variant calling. This input file will be run through haplotypecaller and deepvariant. (default: None)

Option is required.

--pb-model-file PB_MODEL_FILE

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

--out-prefix OUT_PREFIX

Prefix filename for output data. (default: None)

Option is required.

Options specific to this tool

--disable-deepvariant: Generate results for haplotypecaller only. (default: None)
--disable-haplotypecaller: Generate results for deepvariant only. (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 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: -standard-min-confidence-threshold-for-calling 30)
--static-quantized-quals [STATIC_QUANTIZED_QUALS [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_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 MAX_ALTERNATE_ALLELES: Maximum number of alternate alleles to genotype. (default: None)
-G ANNOTATION_GROUP, --annotation-group 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 [GVCF_GQ_BANDS ...]], --gvcf-gq-bands [GVCF_GQ_BANDS [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: Don't use soft clipped bases for variant calling. (default: None)
--ploidy PLOIDY: Ploidy assumed for the bam file. Currently only haploid (ploidy 1) and diploid (ploidy 2) are supported. (default: 2)
--glnexus-options GLNEXUS_OPTIONS: Pass supported GLnexus options as one string. e.g. --glnexus-options="--list --squeeze". (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)
--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 the installation directory.
--no-seccomp-override: Do not override seccomp options for docker (default: None).
--version: View compatible software versions.

GPU options:

--num-gpus NUM_GPUS: Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used.
--gpu-devices GPU_DEVICES: 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.