Variants & FASTQ / VCF to table
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One row per site (one row per sample in the long layout); columns are the fixed columns, INFO fields, split annotation columns and sample fields. In the wide layout sample columns are named “sample:field”.
Values match bcftools query: missing values and absent flags are written as “.”, present flags as 1, and multi-value fields (such as DP4 and AD) keep their comma-separated text.
With “Split the ANN/EFF annotation” ticked, the first functional annotation is split into allele, effect, impact, gene name, HGVS and other columns, handy for picking missense or high-impact variants.
The downloaded CSV opens in Excel or can be passed on to our table filter and group summary tools.
Values follow bcftools query (Danecek et al. 2021, GigaScience 10:giab008), checked cell by cell; ANN is split per the SnpEff annotation format (Cingolani et al. 2012, Fly 6:80).
Runs in your browser; uncompressed VCF files up to roughly 100 MB are recommended.
Send us your data and research question and you will receive a written plan within 1 working day: analysis steps, parameter rationale, deliverables and timeline. Quoted per project.