GATK4 Best Practice Nextflow Pipeline

GATK4 Best Practice Nextflow Pipeline is a variant calling pipeline for human whole genome sequencing based on the GATK best practice.

Requirements

• NextFlow
• Docker

Running the pipeline

There is no need to download the code explicitly. Nextflow seamlessly intergrates with GitHub with the following command.

nextflow run oliverSI/GATK4_Best_Practice --fastq1 read_R1.fastq.gz --fastq2 read_R2.fastq.gz

N E X T F L O W  ~  version 0.25.6
Launching `main.nf` [cheesy_roentgen] - revision: 2ba478ba4b
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GATK4 Best Practice Nextflow Pipeline (v0.1)                        
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[warm up] executor > local
[89/1d86be] Submitted process > get_phase1_SNPs
[74/369556] Submitted process > get_reference
[d8/8ace49] Submitted process > get_omni
[6b/a2f67e] Submitted process > get_dbSNP
[14/831c24] Submitted process > get_golden_indel
[ea/1836b3] Submitted process > get_hapmap
[6a/b862c1] Submitted process > get_BWA_index
[ad/adb689] Submitted process > BWA
[15/7d3a72] Submitted process > BWA_sort
[9a/56cc98] Submitted process > MarkDuplicates
[11/7b55c6] Submitted process > BaseRecalibrator
[e0/984db2] Submitted process > ApplyBQSR
[43/c70b8e] Submitted process > HaplotypeCaller
[c2/30fac6] Submitted process > GenotypeGVCFs
[84/74b170] Submitted process > VariantRecalibrator_SNPs
[31/37e241] Submitted process > ApplyVQSR_SNPs
[9e/a29311] Submitted process > VariantRecalibrator_INDELs
[29/98dfcd] Submitted process > ApplyVQSR_INDELs
[3b/7de781] Submitted process > copy

Reference sequences(GRCh37/hg19) are automatically imported form Docker Hub.

Pipeline parameters

nextflow run oliverSI/GATK4_Best_Practice --help

N E X T F L O W  ~  version 0.25.5
Launching `main.nf` [silly_baekeland] - revision: 82d1c9f7ca
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GATK4 Best Practice Nextflow Pipeline (v0.1)                        
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USAGE: 
 
nextflow run oliverSI/GATK4_Best_Practice --fastq1 read_R1.fastq.gz --fastq2 read_R2.fastq.gz
 
Mandatory arguments:
    --fastq1        FILE               Fastq(.gz) file for read1
    --fastq2        FILE               Fastq(.gz) file for read2
 
Optional arguments:
    --outdir        DIR                Output directory(default: ./Results)
    --samplename    STRING             Sample name(dafault: fastq1 basename)
    --rg            STRING             Read group tag(dafault: fastq1 basename)
 
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