Nextflow pipeline for the identification of Single Nucleotide Variants (SNVs) from short-read sequences.
This workflow is designed to detect germline variants across multiple samples simultaneously. The steps include:
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Sequence Chunk Creation: Generate sequence chunks based on the FastA Index (FAI) file from the reference genome.
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Parallel SNV and Indel Calling: Utilize a variant caller to identify SNVs and Indels independently on each sequence chunk, leveraging parallel processing.
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Results Merging: Combine the results from individual variant calling processes into a unified dataset.
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Annotation with Annovar: Enhance the variant calls by annotating the results using Annovar, providing additional biological context.
Feel free to customize and extend this pipeline to suit your specific requirements.