somatic

Run a somatic variant pipeline workflow.

The somatic pipeline processes 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.

../../_images/somatic.png

Quick Start

# 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

somatic Reference

Run the tumor normal somatic pipeline from FASTQ to VCF.

Input/Output file options

--ref REF

Path to the reference file. (default: None)

Option is required.

--in-tumor-fq [IN_TUMOR_FQ [IN_TUMOR_FQ ...]]

Path to the pair-ended FASTQ files followed by optional read group with quotes (Example: "@RGtID:footLB:lib1tPL:bartSM:20"). The files can be in fastq or fastq.gz format. 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-tumor-fq sampleX_1_1.fastq.gz sampleX_1_2.fastq.gz --in-tumor-fq sampleX_2_1.fastq.gz sampleX_2_2.fastq.gz. Example 2: --in-tumor-fq sampleX_1_1.fastq.gz sampleX_1_2.fastq.gz "@RG ID:footLB:lib1tPL:bartSM:sm_tumortPU:unit1" --in-tumor-fq sampleX_2_1.fastq.gz sampleX_2_2.fastq.gz "@RG ID:foo2tLB:lib1tPL:bartSM:sm_tumortPU:unit2". For the same sample, Read Groups should have the same sample name (SM) and a different ID and PU. (default: None)

--in-se-tumor-fq [IN_SE_TUMOR_FQ [IN_SE_TUMOR_FQ ...]]

Path to the single-ended FASTQ file followed by an optional read group with quotes (Example: "@RGtID:footLB:lib1tPL:bartSM:sampletPU:foo"). The file must be in fastq or fastq.gz format. Either all sets of inputs must have a read group or none should have it; if no read group is provided one will be added automatically by the pipeline. This option can be repeated multiple times. Example 1: --in-se-tumor-fq sampleX_1.fastq.gz --in-se-tumor-fq sampleX_2.fastq.gz . Example 2: --in-se-tumor-fq sampleX_1.fastq.gz "@RGtID:footLB:lib1tPL:bartSM:tumortPU:unit1" --in-se-tumor-fq sampleX_2.fastq.gz "@RGtID:foo2tLB:lib1tPL:bartSM:tumortPU:unit2" . For the same sample, Read Groups should have the same sample name (SM) and a different ID and PU. (default: None)

--in-normal-fq [IN_NORMAL_FQ [IN_NORMAL_FQ ...]]

Path to the pair-ended FASTQ files followed by an optional read group with quotes (Example: "@RGtID:footLB:lib1tPL:bartSM:20"). The files must be in fastq or fastq.gz format. Either all sets of inputs must have a read group or none should have it; if no rad group is provided one will be automatically added by the pipeline. This option can be repeated multiple times. Example 1: --in-normal-fq sampleX_1_1.fastq.gz sampleX_1_2.fastq.gz --in-fq sampleX_2_1.fastq.gz sampleX_2_2.fastq.gz . Example 2: --in-normal-fq sampleX_1_1.fastq.gz sampleX_1_2.fastq.gz "@RG ID:footLB:lib1tPL:bartSM:sm_normaltPU:unit1" --in-normal-fq sampleX_2_1.fastq.gz sampleX_2_2.fastq.gz "@RG ID:foo2tLB:lib1tPL:bartSM:sm_normaltPU:unit2". For the same sample, Read Groups should have the same sample name (SM) and a different ID and PU. (default: None)

--in-se-normal-fq [IN_SE_NORMAL_FQ [IN_SE_NORMAL_FQ ...]]

Path to the single-ended FASTQ file followed by optional read group with quotes (Example: "@RGtID:footLB:lib1tPL:bartSM:sampletPU:foo"). The file must be in fastq or fastq.gz format. Either all sets of inputs must have a read group or none should have it; if absent it will be added automatically by the pipeline. This option can be repeated multiple times. Example 1: --in-se-normal-fq sampleX_1.fastq.gz --in-se-normal-fq sampleX_2.fastq.gz . Example 2: --in-se-normal-fq sampleX_1.fastq.gz "@RGtID:footLB:lib1tPL:bartSM:normaltPU:unit1" --in-se-normal-fq sampleX_2.fastq.gz "@RGtID:foo2tLB:lib1tPL:bartSM:normaltPU:unit2" . For the same sample, Read Groups should have the same sample name (SM) and a different ID and PU. (default: None)

--knownSites KNOWNSITES

Path to a known indels file. The file must be in vcf.gz format. This option can be used multiple times. (default: None)

--interval-file INTERVAL_FILE

Path to an interval file in one of these 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)

--out-vcf OUT_VCF

Path of VCF file after Variant Calling. (default: None)

Option is required.

--out-tumor-bam OUT_TUMOR_BAM

Path of BAM file for tumor reads. (default: None)

Option is required.

--out-normal-bam OUT_NORMAL_BAM

Path of BAM file for normal reads. (default: None)

--out-tumor-recal-file OUT_TUMOR_RECAL_FILE

Path of the report file after Base Quality Score Recalibration for tumor sample. (default: None)

--out-normal-recal-file OUT_NORMAL_RECAL_FILE

Path of the report file after Base Quality Score Recalibration for normal sample. (default: None)

Tool Options:

-L INTERVAL, --interval INTERVAL

Interval within which to call bqsr 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)

--bwa-options BWA_OPTIONS

Pass supported bwa mem options as one string. The current original bwa mem supported options are -M, -Y, -T (e.g. --bwa-options="-M -Y") (default: None)

--no-warnings

Suppress warning messages about system thread and memory usage. (default: None)

--no-markdups

Do not perform the Mark Duplicates step. Return BAM after sorting. (default: None)

--fix-mate

Add mate cigar (MC) and mate quality (MQ) tags to the output file. (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. (default: None)

--markdups-picard-version-2182

Assume marking duplicates to be similar to Picard version 2.18.2. (default: None)

--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. (default: None)

-ip INTERVAL_PADDING, --interval-padding INTERVAL_PADDING

Amount of padding (in base pairs) to add to each interval you are including. (default: None)

--ploidy PLOIDY

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

--max-mnp-distance MAX_MNP_DISTANCE

Two or more phased substitutions separated by this distance or less are merged into MNPs. (default: 1)

--mutectcaller-options 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 TUMOR_READ_GROUP_SM

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

--tumor-read-group-lb TUMOR_READ_GROUP_LB

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

--tumor-read-group-pl TUMOR_READ_GROUP_PL

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

--tumor-read-group-id-prefix 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 NORMAL_READ_GROUP_SM

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

--normal-read-group-lb NORMAL_READ_GROUP_LB

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

--normal-read-group-pl NORMAL_READ_GROUP_PL

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

--normal-read-group-id-prefix 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)

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.