Question: Size of typical genomic data
0
gravatar for Nicolas Rosewick
5 months ago by
Belgium, Brussels
Nicolas Rosewick6.7k wrote:

Hi,

I'm preparing some slides and would like to have some uptodate information related to typical sizes of NGS applications (VCF and BAM) e.g. exome ; WGS ; RNA-Seq ; gene panels , etc...

Looking in the litterature that's what I found (for 30x coverage and 2x100bp read length)

Type of NGS                   VCF        BAM
Gene panels (50 genes)       1 MB    ~100 MB
Gene panels (500 genes)     10 MB      ~1 GB
Whole Exome                   1Gb      ~5 GB
Whole Genome               125 GB    ~100 GB

Any input ?

Thanks

genomic size • 522 views
ADD COMMENTlink modified 5 months ago by toralmanvar650 • written 5 months ago by Nicolas Rosewick6.7k

VCF only contains variants, as bam files contains all reads alignments, VCF are therefore much smaller than bams. Even for whole genomes you don't expect to have a 125Gb VCF for a 100Gb bam.

More generally, the size of the NGS files are correlated with the size of the species genome, and with the depth of sequencing.

ADD REPLYlink modified 5 months ago • written 5 months ago by guillaume.rbt450

I took this information from A: What Is The Expected Size Of A Whole Genome Vcf And Bcf?

ADD REPLYlink written 5 months ago by Nicolas Rosewick6.7k

I guess the calcul assumes that there is a variant at every position of the human genomes, which never happens.

ADD REPLYlink written 5 months ago by guillaume.rbt450

It is tough to generalize the file size for any of the mentioned analysis. And yes, guillaume.rbt is right, size of vcf for human genome can never reach upto 125 Gb for human.

ADD REPLYlink written 5 months ago by toralmanvar650

It is quite difficult to put numbers on this. To give an idea, though, when I was working in a clinical genetics testing laboratory in the UK National Health Service, we had throughput of around 16 samples per week and panels looking at ~25 genes. In 18 months of NGS testing, we accumulated 6.2TB of data, 1.2TB of which was just the results files (BAM, VCF, text-based reports).

My laboratory manager and I published a report in 'StorageNewsletter' but they now appear to require as subscription even to read it. I have it as PDF if you want it.

ADD REPLYlink written 5 months ago by Kevin Blighe30k
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