Session 2 - Variant calling analysis

Varian Calling

Variant calling entails identifying single nucleotide polymorphisms (SNPs) and small insertions and deletion (indels) from next generation sequencing data. This tutorial will cover SNP and Indel detection in germline cells. Other more complex rearrangements (such as Copy Number Variations) require additional analysis not covered in this tutorial.

Public data

https://www.genome.gov/10001688/international-hapmap-project

Reference HapMap Trio:

https://www.nist.gov/programs-projects/genome-bottle

WGS = Whole Genome Sequencing

WES = Whole Exome Sequencing

Variant calling pipeline : https://nf-co.re/sarek/3.2.3

This guide provides a step-by-step guide to:

1) convert BAM files (i.e., public) to paired-end FASTQ files; and

2) run the nextflow nf-core/sarek variant calling pipeline for whole exome sequencing (WES) datasets.

Pre-requisites:

This user guide assumes that you have already installed conda/miniconda3 and nextflow. If you have not done this yet, follow the instructions below:

• Conda installation: https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html

• wget https://repo.anaconda.com/miniconda/Miniconda3-py37_22.11.1-1-Linux-x86_64.sh
  bash Miniconda3-py37_22.11.1-1-Linux-x86_64.sh

• nextflow installation: NextFlow quick start

• VCFtools: https://vcftools.github.io/man_latest.html

Create a Conda environment with tools needed for downstream analyses

Log into the HPC using your user credentials. To install tools, we will use an interactive PBS session:

qsub -I -S /bin/bash -l walltime=10:00:00 -l select=1:ncpus=2:mem=4gb

Create a Python 3.7 environment:

conda create --name liver python=3.7

Activate the conda environment:

conda activate liver

Then you can install one tool at a time or provide a list (see below); however, installing a list of tools may take a while.

We will use samtools and bcftools for the first part of the tutorial. Run the following commands:

conda install -c bioconda samtools

conda install -c bioconda bedtools

To install several tools, prepare a file called environment.yml (example below). Tip: use a text editor (i.e., vim, nano, or other) to copy and paste the code below into the file.

channels:
  - bioconda
  - conda-forge
dependencies:
  - seqkit
  - vcftools
  - bcftools
  - emboss

Run the following command to install additional tools

conda env update --file environment.yml

To deactivate the conda environment, run:

conda deactivate

Convert BAM to FASTQ

Move to the folder where all the BAM files are present and prepare the following script (i.e., launch_BAM2FASTQ.pbs):

#!/bin/bash -l
#PBS -N BAM2FASTQ
#PBS -l walltime=24:00:00
#PBS -l mem=8gb
#PBS -l ncpus=4

cd $PBS_O_WORKDIR

#activate the conda environment with the necessary tools
conda activate liver

#Sort reads in BAM file by indentifier-name (-n) using 4 CPUs (-@ 4). Note 'prefix' for sorted file noted after $i (input BAM file)
for i in `ls --color=never *.bam`
do
  echo $i
  samtools sort -@ 4 -n $i ${i%%.bam}_sorted
done

#Extract paired end reads in FASTQ format
for file in `ls --color=never *sorted.bam`
do
  echo $file
  bedtools bamtofastq -i $file -fq ${file%%.bam}_R1.fastq -fq2 ${file%%.bam}_R2.fastq
  #compress FASTQ files to run using the sarek pipeline
  gzip -c -9 ${file%%.bam}_R1.fastq > ${file%%.bam}_R1.fastq.gz
  gzip -c -9 ${file%%.bam}_R1.fastq > ${file%%.bam}_R2.fastq.gz
done

Submit the job to the PBS scheduler:

qsub launch_BAM2FASTQ.pbs

Check the submitted job(s):

qjobs

Run variant calling using the nextflow nf-core/sarek pipeline

source: https://nf-co.re/sarek/3.1.2

To run Sarek 3 files are required:

1. launch.pbs → details on how to run the workflow

2. ~/.nextflow/config → specify how to run the workflow in the HPC

3. samplesheet.csv → provides information on the samples and data to be used (i.e., FASTQ, BAM or CRAM)

We will run the Sarek pipeline in three phases:

• Phase I: Preprocessing, mapping, markduplicates, recalibrate

• Phase II: Variant calling

• Phase III: Annotation

PHASE I - preprocessing

Below is an example of a launch_phase1.pbs file for mapping onto the selected genome:

#!/bin/bash -l
#PBS -N sarek_I
#PBS -l walltime=48:00:00
#PBS -l select=1:ncpus=1:mem=5gb
cd $PBS_O_WORKDIR
NXF_OPTS='-Xms1g -Xmx4g'
module load java

#specify the nextflow version to use to run the workflow
export NXF_VER=22.06.1-edge

#run the prepocessing tasks
nextflow run nf-core/sarek \
        -r 3.1.1 \
        -profile singularity \
        --genome GATK.GRCh38 \
        --input samplesheet.csv

~/.nextflow/config file: (Note: You may already have this file if you installed Nextflow using this guide )

singularity {
    cacheDir = '$HOME/NXF_SINGULARITY_CACHEDIR'
    autoMounts = true
}

conda {
    cacheDir = '$HOME/NXF_CONDA_CACHEDIR'
}

singularity {
    enabled = true
    autoMounts = true
}

process {
  executor = 'pbspro'
  beforeScript = {
      """
      source $HOME/.bashrc
      source $HOME/.profile
      """
  }
  scratch = false
  cleanup = false
}

Example of a samplesheet.csv file:

patient,sample,lane,fastq_1,fastq_2
healthy_11,1,1,/path/to/data/1.Healthy/Healthy_Combined_11_sorted_R1.fastq.gz,/path/to/data/1.Healthy/Healthy_Combined_11_sorted_R2.fastq.gz

Prepare a samplesheet.csv file that contains the information of all the samples to be processed. Once ready, submit the job to the PBS scheduler:

qsub launch_phase1.pbs

PHASE II - variant calling

Prepare/edit the following launch_phase2.pbs script:

#!/bin/bash -l
#PBS -N sarek_II
#PBS -l walltime=48:00:00
#PBS -l select=1:ncpus=1:mem=5gb
cd $PBS_O_WORKDIR
NXF_OPTS='-Xms1g -Xmx4g'
module load java

#specify the nextflow version to use to run the workflow
export NXF_VER=22.06.1-edge

#run the sarek pipeline
nextflow run nf-core/sarek \
        -r 3.1.1 \
        -profile singularity \
        --genome GATK.GRCh38 \
        --step variant_calling \
        --tools haplotypecaller \
        --wes \
        -resume

Note: Sarek will automatically detect the input for the variant calling phase based on the results from the phase 1 outputs (i.e., results/csv/recalibrate.csv)

Submit the job to the PBS scheduler:

qsub launch_phase2.pbs

monitor the progress on the HPC:

qjobs

Alternatively, view the progress of the submitted job on the Nextflow Tower.

PHASE III - annotation

Download the singularity container for VEP in your catched Nextflow Singularity folder

singularity pull  --name nfcore-vep-106.1.GRCh38.img docker://nfcore/vep:106.1.GRCh38

Prepare/edit the following launch_phase3.pbs script:

#!/bin/bash -l
#PBS -N sarek_III
#PBS -l walltime=48:00:00
#PBS -l select=1:ncpus=1:mem=5gb
cd $PBS_O_WORKDIR
NXF_OPTS='-Xms1g -Xmx4g'
module load java

#specify the nextflow version to use to run the workflow
export NXF_VER=22.06.1-edge

#run the sarek pipeline
nextflow run nf-core/sarek \
        -r 3.1.1 \
        -profile singularity \
        --genome GATK.GRCh38 \
        --step annotate \
        --tools vep,snpeff \
        --wes \
        -resume

Similarly to Phase 2, the Sarek pipeline will automatically detect the VCF input file for running annotation using the selected tool(s).

Submit the job to the PBS scheduler:

qsub launch_phase3.pbs

monitor the progress on the HPC:

qjobs

Alternatively, view the progress of the submitted job on the Nextflow Tower.