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.
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.
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 |
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.
Non-variant regions normal font while variants are bold.
Upload your WGS data to use this app. If you haven't yet taken a DNA test, order one of our DNA tests.
Once your DNA data is stored in your Sequencing.com account, click the app's 'Start' button. You'll receive your results in about 15 minutes.
Test Compatibility | Format Compatibility | Reference Genome Compatibility | |||
---|---|---|---|---|---|
Whole Genome Sequencing | BAM | hg38 / GRCh38 | |||
Exome Sequencing | hg19 / GRCh37 | ||||
Ultimate DNA Test | hg18 / GRCh36 | ||||
23andMe | hg17 / GRCh35 | ||||
AncestryDNA | |||||
MyHeritage | |||||
Dante Labs | |||||
Nebula Genomics | |||||
Genes for Good | |||||
Living DNA | |||||
HomeDNA | |||||
FTDNA | |||||
Silverberry Genomix | |||||
Toolbox Genomics | |||||
Full Genomes | |||||
Color | |||||
New Amsterdam Genomics | |||||
24Genetics | |||||
Vitagene | |||||
Helix | |||||
Genos | |||||
tellmeGen | |||||
GSA | |||||
Axiom | |||||
almost all other genetic tests |
Ultimate DNA Test |
Ultimate Genome Sequencing |
|
---|---|---|
Discounted Price | $69 |
$399 |
Amount of genome tested | 1% | 100% |
Technology | Enhanced Genotyping Microarray | Clinical-Grade 30x Genome Sequencing |
$19.99 per use