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.
BAMs stay on this computer. Only local file paths and the small CSV plan reach this local app.
1 Input
A new BAM is written here. The original BAM is never used as the output.
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.
Left position is the last base kept from the 5′ partner; right position is the first base
kept from the 3′ partner. Strand is the strand each partner contributes on.
3 Run
Verification is on by default. Review achieved read count/VAF and all warnings before using the control.
Result
Nothing run yet.
1 CSV plan
No plan selected.
The browser reads this small plan as text. It does not read or upload BAM contents.
2 Local folders
Relative input_bam paths in the CSV are resolved beneath this folder.
Blank output_bam cells are written here as <sample>.spiked.bam.
Batch preview and progress
Choose a CSV plan, then validate it before starting.