DEEPVARIANT GERMLINE PIPELINE

Given one or more pairs of fastq files, you can run the germline variant pipeline workflow to generate output including variants, BAM, and recal.

The deepvariant germline pipeline includes alignment, sorting, marking, and deepvariant variant caller. Currently, Deepvariant is supported for T4, V100, and A100 GPUs. The inputs are BWA-indexed reference files, pair-ended fastq files. The outputs of this pipeline are:

  • Aligned, co-ordinate sorted, duplicated marked bam

  • Variants in vcf/g.vcf/g.vcf.gz format

../_images/deep.png

Options

--ref

(required) The reference genome in fasta format. We assume that the indexing required to run bwa has been completed by the user.

--in-fq

(required) Pair ended fastq files. These can be in .fq.gz or .fastq.gz format. You can provide multiple pairs as inputs like so:... --in-fq $fq1 $fq2 --in-fq $fq3 $fq4 ...

--in-se-fq

(required) Single ended fastq files. These can be in .fastq or .fastq.gz format. You can provide read group information as an optional third argument.

Example 1:

--in-se-fq sampleX.fastq.gz

Example 2:

--in-se-fq sampleX.fastq.gz "@RG\tID:foo\tLB:lib1\tPL:bar\tSM:sample\tPU:unit1"

This option can be repeated multiple times as well.

Example 1:

--in-se-fq sampleX_1.fastq.gz --in-se-fq sampleX_2.fastq.gz

Example 2:

--in-se-fq sampleX_1.fastq.gz "@RG\tID:foo\tLB:lib1\tPL:bar\tSM:sample\tPU:unit1" \ --in-se-fq sampleX_2.fastq.gz "@RG\tID:foo2\tLB:lib1\tPL:bar\tSM:sample\tPU:unit2"

Either all sets of inputs have read group or none should have it and will be automatically added by the pipeline. For the same sample, Read Groups should have the same sample name (SM) and different ID and PU.

--out-bam

(required) Path to the file that will contain BAM/CRAM output.

--out-variants

(required) Name of VCF/GVCF/GVCF.GZ file after Variant Calling. Absolute or relative path can be given.

--no-markdups

Defaults to False.

Do not mark duplicates, generate bam after co-ordinate sorting.

--out-duplicate-metrics

Path of duplicate metrics file after Marking Duplicates.

--markdups-assume-sortorder-queryname

Assume the reads are sorted by queryname for Marking Duplicates. This will mark secondary, supplementary and unmapped reads as duplicates as well. This flag will not impact variant calling while increasing processing times.

--optical-duplicate-pixel-distance

The maximum offset between two duplicate clusters in order to consider them optical duplicates. Ignored if –out-duplicate-metrics is not passed.

--read-group-sm

SM tag for read groups in this run.

--read-group-lb

LB tag for read groups in this run.

--read-group-pl

PL tag for read groups in this run.

--read-group-id-prefix

Prefix for ID and PU tag for read groups in this run. This prefix will be used for all pair of fastq files in this run. The ID and PU tag will consist of this prefix and an identifier which will be unique for a pair of fastq files.

--interval-file

Path to an interval file for BQSR step with possible formats: Picard-style (.interval_list or .picard), GATK-style (.list or .intervals), or BED file (.bed). This option can be used multiple times (default: None)

--interval

(-L) Interval strings within which to call variants from the input reads. Overlapping intervals will be combined. Interval files should be passed using the –interval-file option. This option can be used multiple times. e.g. -L chr1 -L chr2:10000 -L chr3:20000+ -L chr4:10000-20000 (default: None)

--gvcf

Defaults to False.

Generate variant calls in gVCF format. Final output will have .g.vcf extension.

--bwa-options

Pass supported bwa mem options as one string. Current original bwa mem supported options, -M, -Y, -T. e.g. –bwa-options “-M -Y” (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 run time (default: Allele Count Linear)

--knownSites KNOWNSITES

Path to a known indels file. Must be in vcf/vcf.gz format. This option can be used multiple times.

--markdups-picard-version-2182

Assume marking duplicates to be similar to Picard version 2.18.2.

--no-warnings

Suppress warning messages about system thread and memory usage.

--optical-duplicate-pixel-distance OPTICAL_DUPLICATE_PIXEL_DISTANCE

The maximum offset between two duplicate clusters in order to consider them optical duplicates. Ignored if –out-duplicate-metrics is not passed.

--out-recal-file OUT_RECAL_FILE

Path of report file after Base Quality Score Recalibration. Path can be a Google Cloud Storage object or AWS S3 Storage object.

--pb-model-file PB_MODEL_FILE

Path of non-default parabricks model file for deepvariant.

--norealign-reads

Do not locally realign reads before calling variants. Reads longer than 500 bp are never realigned (default: None)

--sort-by-haplotypes

Reads are sorted by haplotypes (using HP tag) (default: None)

--keep-duplicates

Keep reads that are duplicate (default: None)

--vsc-min-count-snps

SNP alleles occurring at least this many times in our AlleleCount will be advanced as candidates (default: 2)

–vsc-min-count-indels Indel alleles occurring at least this many times in our AlleleCount will be advanced as candidates (default: 2)

--vsc-min-fraction-snps

SNP alleles occurring at least this fraction of all counts in our AlleleCount will be advanced as candidates (default: 0.12)

–vsc-min-fraction-indels Indel alleles occurring at least this fraction of all counts in our AlleleCount will be advanced as candidates (default: None)

--min-mapping-quality

By default, reads with any mapping quality are kept. Setting this field to a positive integer i will only keep reads that have a MAPQ >= i. Note this only applies to aligned reads (default: 5)

–min-base-quality Minimum base quality. This field indicates that we are enforcing a minimum base quality score for alternate alleles. Alternate alleles will only be considered if all bases in the allele have a quality greater than min_base_quality (default: 10)

--mode MODE

Value can be one of [shortread, pacbio, ont]. By default, it is shortread. If mode is set to pacbio, the following defaults are used: –norealign-reads, –alt-aligned-pileup diff_channels, –vsc-min-fraction-indels 0.12. If mode is set to ont, the following defaults are used: -norealign-reads, –variant-caller VCF_CANDIDATE_IMPORTER (default: shortread)

--alt-aligned-pileup

Value can be one of [none, diff_channels]. Include alignments of reads against each candidate alternate allele in the pileup image. Default is none which turns this feature off (default: None)

--variant-caller

Value can be one of [VERY_SENSITIVE_CALLER, VCF_CANDIDATE_IMPORTER]. The caller to use to make examples. If you use VCF_CANDIDATE_IMPORTER, it implies force calling. Default is VERY_SENSITIVE_CALLER

--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.