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.

chr20   287125  .       T       .       .       PASS    END=287136;BLOCKAVG_min30p3a    GT:DP:GQX:MQ    0/0:40:78:40
chr20   287137  .       G       .       .       LowGQX  .       GT:DP:GQX:MQ    0/0:42:11:42
chr20   287138  .       C       .       .       PASS    END=287178;BLOCKAVG_min30p3a    GT:DP:GQX:MQ    0/0:36:96:42
chr20   287179  .       C       T       310.01  PASS    BaseQRankSum=-0.721;DP=37;Dels=0.00;FS=14.994;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.29;MQ0=
0;MQRankSum=-1.091;QD=8.38;ReadPosRankSum=-1.963;SB=-1.901e+01     GT:AD:DP:GQ:PL:MQ:GQX   0/1:24,13:37:99:340,0,810:52:99
chr20   287180  .       G       .       .       PASS    END=287245;BLOCKAVG_min30p3a    GT:DP:GQX:MQ    0/0:32:78:49
chr20   287246  .       G       A       567.01  PASS    BaseQRankSum=-0.718;DP=33;Dels=0.00;FS=5.093;HaplotypeScore=3.2995;MLEAC=1;MLEAF=0.500;MQ=49.01;MQ0=0
;MQRankSum=1.050;QD=17.18;ReadPosRankSum=0.129;SB=-2.920e+02       GT:AD:DP:GQ:PL:MQ:GQX   0/1:13,20:33:99:597,0,343:49:99
chr20   287247  .       C       .       .       PASS    END=287259;BLOCKAVG_min30p3a    GT:DP:GQX:MQ    0/0:27:75:46
chr20   287260  .       C       .       .       PASS    END=287270;BLOCKAVG_min30p3a    GT:DP:GQX:MQ    0/0:26:69:38
chr20   287271  .       T       G       778     PASS    DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=38.49;MQ0=0;QD=29.92;SB=-2.930e+
02 GT:AD:DP:GQ:PL:MQ:GQX   1/1:0,26:26:72:811,72,0:38:72
chr20   287272  .       A       .       .       PASS    END=287285;BLOCKAVG_min30p3a    GT:DP:GQX:MQ    0/0:26:69:34

Citations

  1. Chris Saunders: gvcftools

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.

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Compatible with data from whole genome sequencing services.

 

 

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 Kit

Ultimate DNA Test

Ultimate Genome Sequencing DNA Collection Kit

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Discounted Price $69  $189 $399  $599
     
Amount of genome tested 1% 100%
     
Technology Enhanced Genotyping Microarray Clinical-Grade 30x Genome Sequencing

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