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Variant QC & Filtering
Stage-1 QC and filtering for VCF files. Select an existing OmniObject VCF or upload one, then apply reproducible filters (QUAL/DP/AF/PASS and annotation-aware constraints).
Plugin:
variant_qc_filtering
Input:
VCF / VCF.GZ / VCF.XZ
Output:
filtered VCF + QC report
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Start a run
Select how you want to provide input.
Use OmniObject
Upload VCF
Choose OmniObject
Pick an existing VCF artifact from the OmniObject registry.
VCF object
— Select a VCF OmniObject —
Tip: If you don’t see your file here, use the Upload option.
Upload VCF
Supported:
.vcf
,
.vcf.gz
,
.vcf.xz
.
File
The uploaded VCF is copied into the run workspace before filtering.
QC & filtering settings
These are Stage-1 filters. Keep them conservative to avoid losing clinically relevant variants.
Require PASS filter
No
Yes
Min QUAL
Min DP (INFO/DP)
Max AF (INFO/AF)
Keep only bi-allelic
No
Yes
Keep SNP only
No
Yes
Notes (optional)
Run
Run Variant QC & Filtering
After submission, you’ll be redirected to the run page where you can monitor status and download outputs.