SpikeForge

known variants and fusions, planted into real data

Create research-use synthetic controls from BAM or FASTQ files, then verify exactly what changed. Choose one sample below or validate a CSV plan for a cohort.

Research use only — not for diagnosis, treatment selection, or patient care. Keep the original sequencing files unchanged. SpikeForge outputs are synthetic positive controls and must not enter clinical reporting.

Choose a local path or an HTTPS download link. Linked BAMs download to this computer before processing; SpikeForge never uploads them.

1 Input

Where is the input BAM?

Local BAM pathBrowse within the data folder chosen at startup. Downloadable HTTPS linkDownload and inspect the BAM locally before the run.

Local BAM file path

Only files beneath the data folder selected when SpikeForge started are available.

Output BAM

A new BAM is written here. The original BAM is never used as the output.

Reference FASTA — required for fusions and FASTQ substitution

A substitution in a BAM can be checked from its MD tags when no FASTA is supplied.

2 What to plant

“Add ALT reads” asks for additional edited BAM records. Mates and duplicate families remain together, so the nearest biologically coherent count may differ.

3 Run

Seed

Sample name

Fragment mean

Fragment SD

Truth-file folder (blank = beside the output)

Verification is on by default. Review achieved read count/VAF and all warnings before using the control.

Result

Nothing run yet.

1 CSV plan

CSV or TSV plan

No plan selected.

Each row uses exactly one source: input_bam for a local path or input_url for a direct HTTPS download. Linked BAMs download locally first; no BAM is uploaded.

2 Local folders

Local input root (for input_bam rows)

Relative input_bam paths are resolved beneath this folder. It may be blank when every row uses input_url.

Output root

Blank output_bam cells are written here as <sample>.spiked.bam.

Preparation checks local paths and downloads linked BAMs beneath the working folder selected at startup before validating their headers.

Batch preview and progress

Choose a CSV plan, then validate it before starting.