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Cancer Variant Calling Pipeline

This pipeline is designed for the analysis of tumor samples to identify somatic and germline mutations using next-generation sequencing data. It includes the following steps:

1. Quality Control: Perform quality control on raw sequencing data using FastQC.
2. Trimming: Trim adapter sequences and low-quality reads using Trimmomatic.
3. Alignment: Map trimmed reads to a reference genome using BWA.
4. Sorting and Indexing: Convert aligned reads to BAM format, sort, and index using Samtools.
5. Mark Duplicates: Identify and mark duplicate reads using Picard Tools.
6. Base Recalibration: Correct systematic errors in base quality scores using GATK.
7. Variant Calling: Call variants using HaplotypeCaller from GATK.
8. Variant Filtering: Filter variants for somatic and germline mutations using Mutect2 from GATK.
9. Annotation: Annotate variants with functional and clinical information using SnpEff and ANNOVAR.
10. Prediction of Variant Effects: Predict the functional impact of variants using REVEL.

This pipeline integrates various bioinformatics tools and databases to comprehensively analyze tumor samples and identify potentially pathogenic mutations associated with cancer.

12. I have added a SnakeMake file draft to ensure better operationalization of the pipeline