8 months ago by
Thank you for posting this.
I was about to create a Biostars post asking about free alternatives to GENCOVE, but is there an open version that is free to use?
When I looked around, I thought that the only command line option was for uploading files to the interface:
It looks like there is a free trial, but I am not sure how often I might want to check the GENCOVE imputation results. A slower run-time is acceptable to me - I just want to be able to validate what companies say is acceptable low-coverage WGS data as an independent 3rd party (and verify what genetic data can be considered identifying information).
UPDATE (3/6/2020): It took ~2 weeks (I originally submitted a request for a trail on 2/22/2020, I had a phone call with Gencove on 3/2/2020, and I was able to run the analysis on my first successful sample today), but I was able to submit FASTQ files for free, as promised.
I'l provide another update with some additional analysis of the .vcf file that I downloaded, but I also have the following notes:
- You upload FASTQ files with the Command Line Interface (CLI).
- There is a message about checking if a file is uploaded, but I tried to add new files from a folder with previous files and they weren't recognized (so, all of my first set of files were duplicated).
- There are some caveats with the file formatting (depends upon what is found before "_R1" or "_R2" in your .fastq.gz file, if I understand things correctly), but perhaps this can be changed in the future (along with the file checking bug in the CLI)
- For example, I am not sure if you can delete files after they are uploaded, but you can re-name files by creating a new "Client ID" (and you can save the change my immediately assigning them to a project). This was not immediately obvious to me.
- Also, I don't think the "_1" and "_2" format for paired in read was recognized, but you can force files to be forward and reverse reads by the order they appear under the "Client ID".
- I have concerns about the ancestry and PRS provided in the reports, but I was really only interested in the genotypes in the imputed .vcf file.