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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

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
====================================================================
GATK4 Best Practice Nextflow Pipeline (v0.1)                        
====================================================================
[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
====================================================================
GATK4 Best Practice Nextflow Pipeline (v0.1)                        
====================================================================
 
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)
 
====================================================================