Question: Cost Of Variant Calling A Human Wgs 30X Bam/Cram In The Cloud?
2
gravatar for 14134125465346445
5.3 years ago by
United Kingdom
141341254653464453.4k wrote:

What is the cost of calling variants for a human whole genome sequencing at 30x depth in the cloud?

To be more specific, what is the cost of the following:

  1. Uploading a bam or cram file to the cloud service.
  2. Generating a final vcf.gz with the variant information in it.
  3. Downloading the vcf.gz file.
variant-calling cloud • 2.0k views
ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by 141341254653464453.4k
2
gravatar for Charles Warden
5.3 years ago by
Charles Warden6.6k
Duarte, CA
Charles Warden6.6k wrote:

If the .bam file was provided to you, then you might want to ask that company / core about analysis suggestions. There are many variant annotation programs (SeattleSNP, wANNOVAR, etc.) that are free on the web, but you'll need to call the variants first (using VarScan, GATK, etc.).

There was a paper recently published for STORMSeq:

http://www.stormseq.org/

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0084860;jsessionid=B27ABB65C6015D5709680A7410F23A68

It estimated the cost for processing a WGS sample to be ~$30, starting from the .fastq files and ending with the variant annotations..

Galaxy provides some NGS analysis tools (for free), but you'd probably want to use a local mirror (if possible). Otherwise, it will be very slow (and there may be a maximum time limit, I've never tried to use it for large datasets):

https://usegalaxy.org/

ADD COMMENTlink written 5.3 years ago by Charles Warden6.6k

Thanks, that's a really good paper. It also looks like the software is being maintained and they are keeping up with new versions of variant callers and variant annotation tools.

ADD REPLYlink written 5.3 years ago by 141341254653464453.4k
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