bio-workflows-fastq-to-variants

To call DNA variants from raw FASTQ files, you need a workflow that performs QC, read alignment, BAM processing, and variant calling. This process automates those steps using fastp, bwa-mem2, samtools, and bcftools or GATK to generate a final VCF.

An end-to-end DNA sequencing workflow for exome data should handle QC, alignment, and variant calling. This workflow supports exome projects and offers optional BQSR, utilizing tools like bwa-mem2 and bcftools or GATK to produce high-confidence variant calls.

Yes, this FASTQ to VCF workflow supports both bcftools and GATK for variant calling. It provides a choice between these tools, including joint calling options, to accommodate different analysis preferences and project requirements.

Yes, you need a reference genome to align reads and generate variant calls. If you choose to perform optional BQSR, you also need known-site resources for recalibration to achieve high-confidence variant calls.

Yes, you can use this workflow for whole-genome sequencing data. It is flexible enough to handle both whole-genome and exome projects, automating the end-to-end process from raw FASTQ reads to high-confidence variant calls.