2
$\begingroup$

The publicly available reference panel for GWAS analysis is the 1000 genomes reference panel. The reference panel consists of several populations. However, I am searching for a population-specific publicly available reference panel. I want to perform some analysis like Linkage disequilibrium, inheritance, etc. Now there are some imputation reference panels for the specific populations such as UK10k (European), CAAPA (African), etc.

However, to access this panel we need to go through a lot of agreements and processes. Can anyone give me a list of publicly available population-specific reference panel, preferably, South Asian, European, Eastern Asian, African and Hispanic?

Improve this question
$\endgroup$
4
  • $\begingroup$ Can you describe why one of the populations in the 1000 genomes reference panel won't work for you? $\endgroup$
    – winni2k
    Commented May 31, 2022 at 19:51
  • $\begingroup$ are you telling me to subset the 1000 genome panel? $\endgroup$
    – Shafayet Rahat
    Commented Jun 1, 2022 at 7:14
  • 1
    $\begingroup$ If that's your question then that's a great question. Answer to the question is that, I'm working on low coverage sequencing(<1x). To achieve the expected accuracy on the imputation of a specific population's sample, it's important for me to have samples of more than 1000 in the reference panel. Now, I can subset the 1000 geome panel. However, it consists roughly 400-800 samples per population which is pretty low for my cause. That's why I need reference panel with larger samples. $\endgroup$
    – Shafayet Rahat
    Commented Jun 1, 2022 at 7:18
  • $\begingroup$ Very much all population or nation-specific large reference panels are park of national biobanks and you will not get the genotype-level data without having to do the process of requesting the data , since these are protected in almost all cases, $\endgroup$
    – JRodrigoF
    Commented Jun 17, 2022 at 8:02

0

Reset to default

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Browse other questions tagged or ask your own question.