Are there any variant prioritization tools that handle multiple file formats like FASTQ, BAM, and VCF in one workflow?

Yes—there are workflow systems and integrated pipelines that can take you from FASTQ → BAM → VCF and then do variant prioritization/annotation in the same overall workflow. The key distinction is:

• Variant prioritization tools usually start from VCF.
• End-to-end pipelines handle FASTQ, BAM, and VCF as parts of one workflow.

Common options

1) GATK Best Practices pipelines

• Typical flow: FASTQ → alignment → BAM/CRAM → variant calling → VCF
• Can be combined with annotation/prioritization tools like VEP, SnpEff, ANNOVAR, or custom filtering.
• Good if you want a standard, widely used NGS workflow.

2) nf-core pipelines

Examples:

• nf-core/sarek: DNA variant calling pipeline
• nf-core/rnaseq: RNA-seq, can lead to variant-related outputs in some contexts
• Built with Nextflow, handles multiple input types and supports downstream annotation
• Often integrates VEP, SnpEff, and reporting

3) Galaxy

• Web-based workflow platform that can accept and connect:
  • FASTQ
  • BAM
  • VCF
• You can build one workflow that does alignment, variant calling, annotation, and filtering/prioritization.
• Useful if you want a GUI instead of coding.

4) Seven Bridges / DNAnexus / Terra workflows

• Cloud-based platforms that can orchestrate multi-step pipelines.
• Support end-to-end processing and variant interpretation modules.
• Often used in clinical or large-scale genomics settings.

5) WGS/WES variant interpretation pipelines

Tools/pipelines that include prioritization after calling:

• GEM
• Exomiser
• Variantyx-style clinical workflows
• Moon, Franklin, etc. depending on vendor/platform
• Usually they take VCF plus phenotype data, but are often integrated into larger workflows that begin with FASTQ.

Important note

If your goal is specifically variant prioritization, tools like these usually need:

• VCF
• phenotype information
• inheritance model
• population frequency databases
• functional prediction annotations

They generally do not prioritize directly from FASTQ or BAM alone; those files are typically used upstream to generate the VCF.

Practical recommendation

If you want one workflow that covers everything:

• Nextflow + nf-core/sarek + VEP/Exomiser is a strong open-source option
• Galaxy if you want a no-code/GUI solution
• GATK-based pipeline + annotation tools if you want a more traditional setup

If you want, I can also recommend:

1. open-source tools only,
2. clinical-grade tools, or
3. a specific pipeline for WES/WGS/RNA-seq.