Variant calling

Author

Menachem Sklarz

Affiliation

Bioinformatics Core Facility

Organization

National Institute of Biotechnology in the Negev, Ben Gurion University.

This workflow performs a basic variant-calling analysis.

Steps:

1. Merging the fastq sequences into a single file per sample (merge)

2. Mapping to a reference genome with bowtie2 (bowtie2 module)

3. Sorting, filtering and conversion to BAM with samtools (samtools module)

4. Variant calling with two programs:

   1. freebayes (freebayes module)

   2. mpileup and varscan (mpileup_varscan module)

5. Analysis of the resulting VCF file with VCFtools (vcftools module).

Workflow Schema

Requires

• fastq files, either paired-end or single-end.

Programs required

• FastQC

• trimmomatic

• bowtie2

• samtools

• freebayes

• varscan

• VCFtools

Example of Sample File

Title       ChIP_project

#SampleID   Type    Path    lane
Sample1     Forward /path/to/Sample1_F1.fastq.gz 1
Sample1     Forward /path/to/Sample1_F2.fastq.gz 2
Sample1     Reverse /path/to/Sample1_R1.fastq.gz 1
Sample1     Reverse /path/to/Sample1_R2.fastq.gz 2
Sample2     Forward /path/to/Sample2_F1.fastq.gz 1
Sample2     Reverse /path/to/Sample2_R1.fastq.gz 1
Sample2     Forward /path/to/Sample2_F2.fastq.gz 2
Sample2     Reverse /path/to/Sample2_R2.fastq.gz 2

Download

The workflow file is available here