Question: GWAVA prediction for noncoding variants
0
gravatar for onemoreuser
6 months ago by
onemoreuser10
onemoreuser10 wrote:

GWAVA looks like a good tool to the prediction of the functional impact of non-coding genetic variants (http://www.sanger.ac.uk/science/tools/gwava). But in In the documentation it only mentions support for GRCh37. Does anyone know if there is support for GRCh38? (I tried to send an email to the GWAVA team but the email provided isn't working)

Thank you

ADD COMMENTlink modified 5 months ago by Biostar ♦♦ 20 • written 6 months ago by onemoreuser10

Which email have you tried?

Most of those tools for predicting the deleteriousness / functionality of non-coding variants were built on hg19 / GRCh37 data, unfortunately. I am not sure of their support for hg38.

You may want to look through the other tools to see if they support it:

  • CADD
  • DANN
  • FATHMM-MKL
  • SuRFR
  • PRVCS
  • Genomiser
  • LINSIGHT

Also, in my own opinion, GWAVA actually underperforms on real World data when compared to most of the other tools, but this is because it was mostly trained on TSS variants. Each of these tools targets a particular 'niche', except for CADD, which has broad usage and provides a general 'feel' of what may or may not be functional.

ADD REPLYlink written 6 months ago by Kevin Blighe28k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 757 users visited in the last hour