variant-calling-with-Snakemake-and-GATK 1.0

I am delighted to announce the release of a Snakemake workflow for variant calling using the Genome Analysis Toolkit (GATK) best practices. This pipeline has been developed to process Illumina-generated sequences and can be adapted to suit any organism of interest. Additionally, it is optimized for Plasmodium falciparum, based on a recently published pipeline.

This release comes with several key features, including support for paired-end reads, comprehensive pipeline sections for data processing, mapping, variant calling, and filtering, hard and soft filter options for variant calling, annotation of variants and calculation of allele frequencies.

The pipeline is divided into these sections:

• Compile List of Output Files
• Gather Genome Data
• Perform Fastq Quality Control
• Map Reads to Genome
• Generate Mapping Quality Statistics
• Perform Variant Calling
• Perform Variant Filtering (Hard or Soft)
• Annotate Variants and Calculate Allele Frequencies

For more information on the rules and steps within each section, please refer to the detailed pipeline sections provided in the README file.

I am open to feedback and contributions from the community to enhance and expand this pipeline.