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h3avarcall - H3ABioNet Variant Calling Pipeline

h3avarcall is a Nextflow pipeline developed by H3ABioNet for genomic Variant Calling allowing to detect SNPs and Indels giving raw sequence reads (fastq files) as input. h3avarcall includes the different steps from aligning raw sequence reads to variant calling and filtering using GATK.
For more details about the different steps of the pipeline, check the [H3ABionet SOPs pages] https://h3abionet.github.io/H3ABionet-SOPs/Variant-Calling h3avarcall is a modular and extensible tool allowing users to run the whole pipeline, use only parts of it and also to easily enrich it and adapt it to their needs. h3avarcall generates a number of intermediate files where results from various steps of the pipeline are stored.

1. Obtaining pipeline and preparing Data

First, you need to clone the h3avarcall repository onto you machine:

git clone https://github.com/h3abionet/h3avarcall.git
cd h3avarcall

Content of the repository:

h3avarcall
  |--containers                       ## Folder for Singularity images and recipes (in case you want to build yourself). All downloaded images go here!
  |  |--Singularity.bwa               ## Singularity recipe file for BWA and Samtools.
  |  |--Singularity.fastqc            ## Singularity recipe file for FastQC.
  |  |--Singularity.gatk              ## Singularity recipe file for GATK and tabix.
  |  |--Singularity.trimmomatic       ## Singularity recipe file for Trimmimatic.
  |--gatk-b37-bundle                  ## Folder for stoding downloaded GATK-b37-bundle files.
  |  |--b37_files_minimal.txt         ## LList of GATK-b37-bundle files to be downloaded (bundle TOO BIG! Only selected files needed for the pipeline). 
  |--templates                        ## Folder for extra scripts for the pipeline.
  |  |--download_bundles.sh           ## Script for downloading GATK-b37-bundle.
  |--LICENSE                          ## Duh!
  |--README.md                        ## Duh!
  |--main.config                      ## User configuration file! All inputs, outputs and options GO HERE!! ONLY file that SHOULD be modified by user!
  |--main.nf                          ## Main h3avarcall nextflow scripts.
  |--nextflow.config                  ## Pipeline configuration file! DO NOT EDIT!!!

The main.config file:

/*==================================================================================================
 * THIS FILE IS USED TO SPECIFY INPUT, OUTPUTS AND PARAMETERS. THE FOLLOWING OPTIONS ARE THE ALLOWED:
 * ==================================================================================================
 * data         : Path to where the data is (FASTQ files).
 * out          : Path to store output results.
 * bundle       : GATK-b37-bundle list file.
 * mode         : Worflow step to perform. Can be any of [ do.GetContainers | do.GenomeIndexing | do.QC | do.ReadTrimming | do.ReadAlignment | do.VarianCalling | do.VariantFiltering | do.MultiQC].
 * trim         : Trimming options for Trimmomatic.
 * resources    : Location of the GATK-b37-bundle folder.
 * from         : pipeline step to resume pipeline from. Can be any of [ do.QC | do.ReadTrimming | do.ReadAlignment | do.VarianCalling | do.VariantFiltering ].
 * params.help  : Print help menu.
 * ==================================================================================================
 * BELOW ARE THE DEFAULT PARAMETERS! YOU'RE MORE THAN WELCOME TO CHANGE AS DESIRED!
 * ==================================================================================================
 */

params {
    data         = "$baseDir/data"
    out          = "$baseDir/results"
    bundle       = "$baseDir/gatk-b37-bundle/b37_files_minimal.txt"
    mode         = "do.QC"
    trim         = "ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:8:true TRAILING:28 MINLEN:40"
    resources    = "$baseDir/gatk-b37-bundle"
    from         = null
    params.help  = null
}

1.1. Download test datasets:

Create a data directory under the h3avarcall repository:

mkdir data
cd data

Download the test data from THIS_SITE using one of the commands bellow:

1.1.2. Using LFTP (faster)

lftp -e "pget -n 20 ftp://ftp-trace.ncbi.nih.gov/giab/ftp/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/NIST7035_TAAGGCGA_L001_R1_001.fastq.gz; bye"
lftp -e "pget -n 20 ftp://ftp-trace.ncbi.nih.gov/giab/ftp/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/NIST7035_TAAGGCGA_L001_R2_001.fastq.gz; bye"

1.1.3. Using WGET (slower)

wget ftp://ftp-trace.ncbi.nih.gov/giab/ftp/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/NIST7035_TAAGGCGA_L001_R1_001.fastq.gz
wget ftp://ftp-trace.ncbi.nih.gov/giab/ftp/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/NIST7035_TAAGGCGA_L001_R2_001.fastq.gz

1.2. Download the Singularity containers (required to execute the pipeline):

nextflow run main.nf -profile slurm --mode do.GetContainers

1.3. Download the GATK b37 bundle (required to execute the pipeline):

This step takes FOREVER to run - run it only once!

nextflow run main.nf -profile slurm --mode do.GenomeIndexing

If by some miracle you happen to have access to the WITS Cluster, you do not need to download the GATK-b37-bundle! Simply cd into the gatk-b37-bundle folder of the h3avarcall repo and soft-link the GATK-b37-bundle data as follows:

cd gatk-b37-bundle
ln -s /global/blast/gatk-bundle/b37/* .

2. Executing the main h3avarcall pipeline

2.1. Read QC (optional):

Before getting started with the downstream analysis, it's always good to do some quality checks on your raw sequences to assess the quality of raw sequence data, the fastq files. FastQC tool has been used in this workflow. An html report page will be automatically created for each fastq file. You can load up these html pages in your browser to assess your data through graphs and summary tables.
To perform the QC of your fastq files, you can use this command:

nextflow run main.nf -profile slurm --mode do.QC

2.2. Read Trimming (optional):

After performing the QC of your fastq files, you have an idea about the quality of your reads: some of your reads might not be of a very good quality or the quality might drop at some positions (near the begining or end of reads) across all reads and this requires to clean up your library to minimize biaises in your analysis by filtering poor quality reads and/or trim poor quality bases from our samples. Trimmomatic is the trimming tool that has been used here.
For more information about reads preprocessing, check this page.
To run the trimming step of the h3avarcall pipeline, you can use this command:

nextflow run main.nf -profile slurm --mode do.ReadTrimming

2.3. Read Alignment

Once you have good raw sequences quality, the next step is to map your reads to a reference genome to determine where in the genome the reads originated from. The mapper used in this workflow is BWA. For more information about the read alignement step, check this page

Can be run with --from do.ReadTrimming or --from do.QC depending on whether these steps were run!

nextflow run main.nf -profile slurm --mode do.ReadAlignment

2.4. Variant Calling

This step uses the outputs generated by the Read Alignment STEP! MUST run STEP 2.3 (--mode do.ReadAlignment) before running this step.

nextflow run main.nf -profile slurm --mode do.VariantCalling 

2.5. Variant Filtering

This step uses the outputs generated by the Variant Calling STEP! MUST run STEP 2.4 (--mode do.VariantCalling) before running this step.

nextflow run main.nf -profile slurm --mode do.VariantFiltering 

2.6. Workflow QC (MultiQC - Optional)

This step performs a Quality Check of the different pipeline steps that have been ran. You need to run at least ONE step of the pipeline to be able to run this MultiQC step!

nextflow run main.nf -profile slurm --mode do.MultiQC 

3. Explore h3avarcall results

Assuming you did not change the default output folder (in the main.config file), the resulting files will be found in the results folder of the h3avarcall repository. Resulting files for each of the main pipeline steps (2.1 - 2.5) are grouped in different folders as follows:

- [1] Read QC (optional)         =>    `results/1_QC`
- [2] Read Trimming (optional)   =>    `results/2_Read_Trimming`
- [3] Read Alignment             =>    `results/3_Read_Alignment`
- [4] Variant Calling            =>    `results/4_Variant_Calling`
- [5] Variant Filtering          =>    `results/5_Variant_Filtering`
- [6] MultiQC                    =>    `results/MultiQC`

In each of these folders, a sub-folder "workflow_report" is created. It contains 4 different files (h3avarcall_report.html, h3avarcall_timeline.html, h3avarcall_workflow.dot and h3avarcall_trace.txt) containing detailed information on the resources (CPU, MEMORY and TIME) usage of each process in the different pipeline steps.
The results directory structure within h3avarcall repository can be summarized as below:

h3avarcall
  |--results
  |  |--1_QC
  |  |  |--workflow_report
  |  |  |  |--h3avarcall_report.html
  |  |  |  |--h3avarcall_timeline.html
  |  |  |  |--h3avarcall_workflow.dot
  |  |  |  |--h3avarcall_trace.txt
  |  |  |--<sample_1>_R1.fastqc.html .. <sample_N>_R1.fastqc.html
  |  |  |--<sample_1>_R2.fastqc.html .. <sample_N>_R1.fastqc.html
  |  |--2_Read_Trimming
  |  |  |--workflow_report
  |  |  |  |--h3avarcall_report.html
  |  |  |  |--h3avarcall_timeline.html
  |  |  |  |--h3avarcall_workflow.dot
  |  |  |  |--h3avarcall_trace.txt
  |  |  |--<sample_1>.1P.fastq.gz .. <sample_N>.1P.fastq.gz
  |  |  |--<sample_1>.2P.fastq.gz .. <sample_N>.2P.fastq.gz
  |  |--3_Read_Alignment
  |  |  |--workflow_report
  |  |  |  |--h3avarcall_report.html
  |  |  |  |--h3avarcall_timeline.html
  |  |  |  |--h3avarcall_workflow.dot
  |  |  |  |--h3avarcall_trace.txt
  |  |  |--<sample_1>_md.recal.bam .. <sample_N>_md.recal.bam
  |  |  |--<sample_1>_md.recal.bai .. <sample_N>_md.recal.bai
  |  |--4_Variant_Calling
  |  |  |--workflow_report
  |  |  |  |--h3avarcall_report.html
  |  |  |  |--h3avarcall_timeline.html
  |  |  |  |--h3avarcall_workflow.dot
  |  |  |  |--h3avarcall_trace.txt
  |  |  |--chr_1_genotyped.vcf.gz .. chr_22_genotyped.vcf.gz
  |  |  |--chr_1_genotyped.vcf.gz.tbi .. chr_22_genotyped.vcf.gz.tbi
  |  |--5_Variant_Filtering
  |  |  |--workflow_report
  |  |  |  |--h3avarcall_report.html
  |  |  |  |--h3avarcall_timeline.html
  |  |  |  |--h3avarcall_workflow.dot
  |  |  |  |--h3avarcall_trace.txt
  |  |  |--genome.SNP-recal.vcf.gz
  |  |  |--genome.SNP-recal.vcf.gz.tbi
  |  |--MultiQC
  |  |  |--multiqc_data
  |  |  |--multiqc_report.html
  |--work
  |  |--<There's a lot of folders here! Lets not worry about them for today!>

##We're working on further improving the pipleine and the associated documentation, feel free to share comments and suggestions!

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H3A variant calling pipeline

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