Genome VCF
Developed by Sequencing.com
Easily convert your whole genome sequencing (WGS) files into genome VCF (gVCF) files. Compatible with WGS data from any sequencing provider.
$19.99 per genome
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Convert Your WGS Data To Genome VCF (gVCF) Format
This easy-to-use app generates a gVCF v4.1 file from a BAM file.
While this app is only compatible with WGS data in BAM format, our EvE Premium app also converts files to gVCF v4.2 and can be used with FASTQ, BAM, and CRAM.
gVCF eliminates the ambiguity found with standard VCF by including data for all sites within a genome.
- gVCF clearly differentiates variant, reference and no-calls for every site in the genome
- Unlike standard VCF, a gVCF includes a call for a site even if the call is the same as the reference genome
Generate gVCF files that conform to VCF v4.1 specifications
The gVCFs produced by this app can be used by most tools that are compatible with VCF v4.1. VCF v4.1 is compatible with older bioinformatics tools such as IGV and Tabix. After using this app, you'll be able to use the gVCF with apps at Sequencing.com and will also be able to share and download your gVCF.
To generate gVCF files compatible with VCF v4.2, please use the EvE Premium app.
Default Filters
ID | Type | Description |
|---|---|---|
| LowGQX | site/indel | GQX is less than 20 |
MaxDepth | site/indel | Depth is greater than 3x the mean chromosome depth |
LowQD | site/indel | QD is less than 3.73 |
LowMQ | site | Site MQ is less than 20 |
| HighFS | site | Site FS is greater than 60 |
HighHaplotypeScore | site | Site HaplotypeScore is greater than 13 |
LowMQRankSum | site | Site MQRankSum is less than -12.5 |
LowReadPosRankSum | site | Site ReadPosRankSum is less than -2.386 |
HighIndelFS | indel | Indel FS is greater than 200. |
| LowIndelReadPosRankSum | indel | Indel ReadPosRankSum is less than -20 |
What's the difference between a conventional VCF and a gVCF (genome VCF)?
Conventional VCF files, also known as standard VCF files and regular VCFs, include data for a specific chromosomal coordinate if the variant (alt) allele is detected. Ambiguity arises, however, when a chromosomal coordinate is not included in a VCF because this could mean either the reference allele was detected or there was a no-call at that coordinate.
Our Sequencing Bioinformatics Team believes this ambiguity is not acceptable when differentiating between a reference allele and a no-call can have a significant impact on the interpretation of the data. Because of this, if you've had whole genome sequencing we recommend using your BAM, CRAM, FASTQ, or genome VCF file instead of a standard VCF.
Please note that our entire system, including all DNA analysis apps and reports in our marketplace, work with FASTQ, BAM, and CRAM files. If you have one of these files, there's no need to first generate a genome VCF to use with our DNA analysis apps and reports. Simply start the app with your FASTQ, BAM, or CRAM.
gVCF Example Data
Non-variant regions normal font while variants are bold.
Citations
- Chris Saunders: gvcftools
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