Whole-genome sequencing

Run

Choose how far
to take your reads.

Drop your FASTQ files in, then pick the stage to stop at. Everything up to it runs; everything after is left alone.

01

FASTQ

Raw reads off the sequencer.

Drop FASTQ files here, or click to choose

Input

02

BAM

Reads aligned to the reference.

03

VCF

Variants called from the alignment.

04

Annotated VCF

Variants annotated against current references.

05

Interpretation

Evidence-status findings from a frozen knowledgebase. Not a diagnosis; requires clinical review.

Add your reads, then pick a stage.

Interpret an annotated VCF

Already have variants? Upload the VEP-annotated VCF and the normalised PASS VCF it was annotated from, and the interpretation stage runs on its own — no alignment, no variant calling. Add the final BAM and the filtered VCF beside it and the sample-entry gate and clinical chain run too; add the GVCF and ancestry does. Anything not uploaded simply drops the modules that read it, and the run says which and why. Missing indexes are built automatically.

Annotated VCF (.vcf.gz, required)

Normalised PASS VCF (.vcf.gz, required)

Final BAM (optional; unlocks the clinical chain)

Filtered VCF (.vcf.gz; required beside the BAM)

BAM index (.bai, optional; built here if left out)

GVCF (.g.vcf.gz, optional; ancestry reads it)

Sample identifier

Modules

ACMG secondary findings

Runs against the connected pipeline.

Choose how farto take your reads.

FASTQ

BAM

VCF

Annotated VCF

Interpretation

Previous runs

Interpret an annotated VCF

Choose how far
to take your reads.