Implementation of Genomic Variant Calling Using GATK4, SPARK, WDL, CROMWELL and DOCKER Over Simulated Ebola NGS Dataset.

Ebola genome is manually mutated to contain non-structural as well as structural variants. One ebola genome contains non-structural variants - 10 SNPs, 10 INDELs, 05 TRANSLOCATIONs, 05 INSERSIONs and their reverse complements. Similarly, other two set of mutated genomes contain structural variants. Each set contains seven mutated ebola genome each one for large deletion, insertion, duplication, translocation, inversion, complex variant1 (consecutive three mutations - insertion, duplication and deletion) and complex variants2 (consecutive three mutations - deletion, duplication and deletion). All insertions are novel sequence insertion.