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. 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

QUICK START

# Create a genomics database
pbrun creategenomicsdb –dir <genomics db address>

# Populate the database with data:
pbrun importgvcftodb –dir < genomics db address> --in-gvcf <input GVCF> --in-gvcf <input GVCF> -- in-gvcf <input GVCF>

# Select variants from the database
$ pbrun selectvariants --ref <Reference Genome> -dir < genomics db address> --out-gvcf <output GVCF>

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 output.

--out-variants

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

--tmp-dir

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

--num-gpus

Defaults to number of GPUs in the system.

The number of GPUs to be used for this analysis task.

--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. All intervals will have a padding of 100 to get read records and 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)

--interval-padding

(-ip) Padding size (in base pairs) to add to each interval you are including (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.

--num-gpus

Defaults to number of GPUs in the system. The number of GPUs to be used for this analysis task.

--gpu-devices

Which GPU devices to use for a run. By default, all GPU devices will be used. To set specific GPU devices, enter a comma-separated list of GPU device numbers.