Entering edit mode
5.1 years ago
Nicolas Rosewick 10k
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 ?
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.
I took this information from A: What Is The Expected Size Of A Whole Genome Vcf And Bcf?
I guess the calcul assumes that there is a variant at every position of the human genomes, which never happens.
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.
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.
I would like to have a look at this report, if you could send it please? Thank you
Sorry, the URL ('link') in my message was erroneous (I have fixed it). However, and also, the magazine now requires a subscription. I will upload the report to another location when I get home. Please reply again here to ping me.
Hey, I have added the files here: https://github.com/kevinblighe/BiostarsMisc