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sarek.md

145 lines · bio-research/skills/nextflow-development/references/pipelines/sarek.md at 2574e29

1# nf-core/sarek

3**Version:** 3.7.1

5**Official Documentation:** https://nf-co.re/sarek/3.7.1/

6**GitHub:** https://github.com/nf-core/sarek

8> **Note:** When updating to a new version, check the [releases page](https://github.com/nf-core/sarek/releases) for breaking changes and update the version in commands below.

nf-core/sarek

Version: 3.7.1

Official Documentation: https://nf-co.re/sarek/3.7.1/ GitHub: https://github.com/nf-core/sarek

Note: When updating to a new version, check the releases page for breaking changes and update the version in commands below.

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10## Contents

11- [Test command](#test-command)

12- [Samplesheet format](#samplesheet-format)

13- [Variant calling modes](#variant-calling-modes)

14- [Parameters](#parameters)

15- [Output files](#output-files)

Test command
Samplesheet format
Variant calling modes
Parameters
Output files

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17## Test command

19```bash

20nextflow run nf-core/sarek -r 3.7.1 -profile test,docker --outdir test_sarek

21```

23Expected: ~20 min, creates aligned BAMs and variant calls.

Test command

nextflow run nf-core/sarek -r 3.7.1 -profile test,docker --outdir test_sarek

Expected: ~20 min, creates aligned BAMs and variant calls.

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25## Samplesheet format

Samplesheet format

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27### From FASTQ

28```csv

29patient,sample,lane,fastq_1,fastq_2

30patient1,tumor,L001,/path/to/tumor_L001_R1.fq.gz,/path/to/tumor_L001_R2.fq.gz

31patient1,tumor,L002,/path/to/tumor_L002_R1.fq.gz,/path/to/tumor_L002_R2.fq.gz

32patient1,normal,L001,/path/to/normal_R1.fq.gz,/path/to/normal_R2.fq.gz

33```

From FASTQ

patient,sample,lane,fastq_1,fastq_2
patient1,tumor,L001,/path/to/tumor_L001_R1.fq.gz,/path/to/tumor_L001_R2.fq.gz
patient1,tumor,L002,/path/to/tumor_L002_R1.fq.gz,/path/to/tumor_L002_R2.fq.gz
patient1,normal,L001,/path/to/normal_R1.fq.gz,/path/to/normal_R2.fq.gz

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35### From BAM/CRAM

36```csv

37patient,sample,bam,bai

38patient1,tumor,/path/to/tumor.bam,/path/to/tumor.bam.bai

39patient1,normal,/path/to/normal.bam,/path/to/normal.bam.bai

40```

From BAM/CRAM

patient,sample,bam,bai
patient1,tumor,/path/to/tumor.bam,/path/to/tumor.bam.bai
patient1,normal,/path/to/normal.bam,/path/to/normal.bam.bai

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42### With tumor/normal status

43```csv

44patient,sample,lane,fastq_1,fastq_2,status

45patient1,tumor,L001,tumor_R1.fq.gz,tumor_R2.fq.gz,1

46patient1,normal,L001,normal_R1.fq.gz,normal_R2.fq.gz,0

47```

49`status`: 0 = normal, 1 = tumor

With tumor/normal status

patient,sample,lane,fastq_1,fastq_2,status
patient1,tumor,L001,tumor_R1.fq.gz,tumor_R2.fq.gz,1
patient1,normal,L001,normal_R1.fq.gz,normal_R2.fq.gz,0

status: 0 = normal, 1 = tumor

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51## Variant calling modes

Variant calling modes

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53### Germline (single sample)

54```bash

55nextflow run nf-core/sarek -r 3.7.1 -profile docker \

56 --input samplesheet.csv --outdir results --genome GRCh38 \

57 --tools haplotypecaller,snpeff

58```

Germline (single sample)

nextflow run nf-core/sarek -r 3.7.1 -profile docker \
    --input samplesheet.csv --outdir results --genome GRCh38 \
    --tools haplotypecaller,snpeff

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60### Somatic (tumor-normal pair)

61```bash

62nextflow run nf-core/sarek -r 3.7.1 -profile docker \

63 --input samplesheet.csv --outdir results --genome GRCh38 \

64 --tools mutect2,strelka,snpeff

65```

Somatic (tumor-normal pair)

nextflow run nf-core/sarek -r 3.7.1 -profile docker \
    --input samplesheet.csv --outdir results --genome GRCh38 \
    --tools mutect2,strelka,snpeff

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67### WES (exome)

68```bash

69nextflow run nf-core/sarek -r 3.7.1 -profile docker \

70 --input samplesheet.csv --outdir results --genome GRCh38 \

71 --wes --intervals /path/to/targets.bed \

72 --tools haplotypecaller,snpeff

73```

WES (exome)

nextflow run nf-core/sarek -r 3.7.1 -profile docker \
    --input samplesheet.csv --outdir results --genome GRCh38 \
    --wes --intervals /path/to/targets.bed \
    --tools haplotypecaller,snpeff

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75### Joint germline (cohort)

76```bash

77--tools haplotypecaller --joint_germline

78```

Joint germline (cohort)

--tools haplotypecaller --joint_germline

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80## Parameters

Parameters

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82### Available tools

84**Germline callers:**

85- `haplotypecaller`: GATK HaplotypeCaller

86- `freebayes`: FreeBayes

87- `deepvariant`: DeepVariant (GPU optional)

88- `strelka`: Strelka2 germline

90**Somatic callers:**

91- `mutect2`: GATK Mutect2

92- `strelka`: Strelka2 somatic

93- `manta`: Structural variants

95**CNV callers:**

96- `ascat`: Copy number

97- `controlfreec`: CNV detection

98- `tiddit`: SV calling

100**Annotation:**

101- `snpeff`: Functional annotation

102- `vep`: Variant Effect Predictor

103

Available tools

Germline callers:

haplotypecaller: GATK HaplotypeCaller
freebayes: FreeBayes
deepvariant: DeepVariant (GPU optional)
strelka: Strelka2 germline

Somatic callers:

mutect2: GATK Mutect2
strelka: Strelka2 somatic
manta: Structural variants

CNV callers:

ascat: Copy number
controlfreec: CNV detection
tiddit: SV calling

Annotation:

snpeff: Functional annotation
vep: Variant Effect Predictor

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104### Key parameters

105

106| Parameter | Default | Description |

107|-----------|---------|-------------|

108| `--tools` | - | Comma-separated list of tools |

109| `--genome` | - | `GRCh38`, `GRCh37` |

110| `--wes` | false | Exome mode (requires `--intervals`) |

111| `--intervals` | - | BED file for targeted regions |

112| `--joint_germline` | false | Joint calling for cohorts |

113| `--skip_bqsr` | false | Skip base quality recalibration |

114

Key parameters

Parameter	Default	Description
`--tools`	-	Comma-separated list of tools
`--genome`	-	`GRCh38`, `GRCh37`
`--wes`	false	Exome mode (requires `--intervals`)
`--intervals`	-	BED file for targeted regions
`--joint_germline`	false	Joint calling for cohorts
`--skip_bqsr`	false	Skip base quality recalibration

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115## Output files

116

117```

118results/

119├── preprocessing/

120│ └── recalibrated/ # Analysis-ready BAMs

121│ └── *.recal.bam

122├── variant_calling/

123│ ├── haplotypecaller/ # Germline VCFs

124│ ├── mutect2/ # Somatic VCFs (filtered)

125│ └── strelka/

126├── annotation/

127│ └── snpeff/ # Annotated VCFs

128└── multiqc/

129```

130

Output files

results/
├── preprocessing/
│   └── recalibrated/           # Analysis-ready BAMs
│       └── *.recal.bam
├── variant_calling/
│   ├── haplotypecaller/        # Germline VCFs
│   ├── mutect2/                # Somatic VCFs (filtered)
│   └── strelka/
├── annotation/
│   └── snpeff/                 # Annotated VCFs
└── multiqc/

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131## Troubleshooting

132

133**BQSR fails**: Check known sites available for genome. Skip with `--skip_bqsr` for non-standard references.

134

135**Mutect2 no variants**: Verify tumor/normal pairing in samplesheet (check `status` column).

136

137**Out of memory**: `--max_memory '128.GB'` for WGS.

138

139**DeepVariant GPU**: Ensure NVIDIA Docker runtime configured.

140