NERVAC

DNA short read sequencing is via this software mapped to a existing reference genome, after that the quality check is done and variants are called based in an interactive configuration file. You can adopt that file as well as the information of your run to your own experiment.

Requirements before starting the pipeline

1. Change the parameters of your own experiment in the folder "config" (config.yml and runinfo.tsv).
2. Set the strictness for your diploid genome in the variant calling step.
3. Install the required packages in a isolated "conda" environment.

This software itself contains multiple steps:

1. Index the reference genome and mapping the short reads to the reference genome.
2. Sort on chromosome name and mark the duplicates.
3. Create via multiple steps a report with alignment and read quality statistics.
   (Optional)
4. Call variants based on the genome like Single Nucleotide Polymorphisms (SNPs), Insertions and Deletions (INDELs) using the aligned reads with specific parameters set in the configuration file (config.yml).
5. Calculate the Alternative Allele Fractions for the populations based on the Variant Call Format (VCF) file, parameters can be changed.
6. Use the annotation from the genome to predict the impact of a certain variant according to their location.