The vast number of data produced by next-generation sequencing (NGS)
techniques poses significant computational challenges and many computational steps are required to translate this output into high-quality results. . Developing a workflow able to perform all stages in an automatic and reliable way is crucial to eliminate manual steps and to speed up result generation.
Here, we present a variant calling workflow executed in a HPC platform, which automatically executes all involved stages in this process using state-of-art software. Briefly, our process includes (a) short-read alignment with a combination of BWA and BFAST aligners, (b) a GATK-based variant calling protocol for indels and SNPs (c) SNP effect predicto to annotate the variants. Our program accepts raw data in Fastq format from Illumina platform and generates a result file with the variants and its biological impact prediction ranked by detection quality score.
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