SOMATIC PIPELINE

Run a somatic variant pipeline workflow

The somatic pipeline process the tumor fastq files and optionally normal fastq files and knownSites files and generates tumor or tumor/normal analysis. The output is in VCF format.

CLI

            

            
# The command line below will run tumor-only analysis.
$ pbrun somatic --ref Ref/Homo_sapiens_assembly38.fasta \
                --in-tumor-fq Data/sample_1.fq.gz Data/sample_2.fq.gz \
                --out-vcf output.vcf \
                --out-tumor-bam tumor.bam

# The command line below will run tumor-normal analysis.
$ pbrun somatic --ref Ref/Homo_sapiens_assembly38.fasta \
                --knownSites Ref/Homo_sapiens_assembly38.known_indels.vcf.gz \
                --in-tumor-fq Data/sample_1.fq.gz Data/sample_2.fq.gz "@RG\tID:sm_tumor_rg1\tLB:lib1\tPL:bar\tSM:sm_tumor\tPU:sm_tumor_rg1" \
                --out-vcf output.vcf \
                --out-tumor-bam tumor.bam \
                --out-tumor-recal-file recal.txt \
                --in-normal-fq normal0.fq.gz normal1.fq.gz "@RG\tID:sm_normal_rg1\tLB:lib1\tPL:bar\tSM:sm_normal\tPU:sm_normal_rg1" \
                --out-normal-bam normal.bam
        

--ref

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

--in-tumor-fq

(required) Full path to the pair ended fastq files (in gz or fastq format) followed by read group with quotes. (Example: "@RG\tID:foo\tLB:lib1\tPL:bar\tSM:20"). Files can be in fastq or fastq.gz format. This option can be repeated multiple times.

--in-se-tumor-fq

Path to the single ended fastq file followed by optional read group with quotes (Example: "@RG\tID:foo\tLB:lib1\tPL:bar\tSM:sample\tPU:foo"). File can be in fastq or fastq.gz format or a google cloud storage object. Either all sets of inputs have read group or none should have it and will be automatically added by the pipeline. This option can be repeated multiple times.

Example 1: --in-se-tumorfq sampleX_1.fastq.gz --in-se-tumor-fq sampleX_2.fastq.gz .

Example 2: --in-se-tumor-fq sampleX_1.fastq.gz "@RG\tID:foo\tLB:lib1\tPL:bar\tSM:tumor\tPU:unit1" --in-se-tumor-fq sampleX_2.fastq.gz "@RG\tID:foo2\tLB:lib1\tPL:bar\tSM:tumor\tPU:unit2" .

For same sample, Read Groups should have same sample name (SM) and different ID and PU (default: None)

--out-vcf

(required) Path of VCF file after Variant Calling.

--out-tumor-bam

(required) Path of bam file for tumor reads.

--out-tumor-recal-file

Path of report file after Base Quality Score Recalibration for tumor sample.

--knownSites

Known indel files in .vcf.gz format. These should be compressed VCF files for known SNPs and indels. You can use this option multiple times. If you provide this option, then you must also provide an –out-recal-file (see below for details).

--in-normal-fq

Full path to the pair ended fastq files (in gz or fastq format) followed by read group with quotes. (Example: "@RG\tID:foo\tLB:lib1\tPL:bar\tSM:20"). Files can be in fastq or fastq.gz format. This option can be repeated multiple times.

--in-se-normal-fq

Path to the single ended fastq file followed by optional read group with quotes (Example: "@RG\tID:foo\tLB:lib1\tPL:bar\tSM:sample\tPU:foo").

File can be in fastq or fastq.gz format or a google cloud storage object. Either all sets of inputs have read group or none should have it and will be automatically added by the pipeline. This option can be repeated multiple times.

Example 1:

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

Example 2:

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

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

For same sample, Read Groups should have same sample name (SM) and different ID and PU (default: None)

--out-normal-bam

Path of bam file for normal reads.

--no-markdups

Defaults to False.

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

--ploidy

Defaults to 2.

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

--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)

--mutectcaller-options

Pass supported mutectcaller options as one string. Currently supported original mutectcaller options: -pcr-indel-model <NONE, HOSTILE, AGGRESSIVE, CONSERVATIVE>. e.g. –mutectcaller- options=”-pcr-indel-model HOSTILE” (default: None)

--tumor-read-group-sm

SM tag for read groups for tumor sample (default: None)

--tumor-read-group-lb

LB tag for read groups for tumor sample (default: None)

--tumor-read-group-pl

PL tag for read groups for tumor sample (default: None)

--tumor-read-group-id-prefix

prefix for ID and PU tag for read groups for tumor sample. This prefix will be used for all pair of tumor 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 (default: None)

--normal-read-group-sm

SM tag for read groups for normal sample (default: None)

--normal-read-group-lb

LB tag for read groups for normal sample (default: None)

--normal-read-group-pl

PL tag for read groups for normal sample (default: None)

--normal-read-group-id-prefix

prefix for ID and PU tag for read groups for normal sample. This prefix will be used for all pair of normal 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 (default: None)

--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)

--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.

--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-normal-recal-file OUT_NORMAL_RECAL_FILE

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

--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.

--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.