denovomutation

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

../../_images/denovo.png

Quick Start

The following command runs the 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

denovomutation Reference

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

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

Dont 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.