Timeline for Chosing an imputation panel for SNP-Chip data?
Current License: CC BY-SA 4.0
7 events
| when toggle format | what | by | license | comment | |
|---|---|---|---|---|---|
| Feb 16, 2022 at 19:47 | comment | added | winni2k | I cannot vouch for these servers, but they are run by reputable groups (my coauthors on the HRC paper in fact): sanger.ac.uk/tool/sanger-imputation-service and imputationserver.sph.umich.edu/index.html#! | |
| Feb 16, 2022 at 16:14 | comment | added | Dan Bolser | can you recommend an imputation server to give me access to HRC and uses HMM-based method such as for example impute2? You seem to be implying that HRC is the largest reference panel out there, but perhaps that's not true... (sorry for my basic questions). | |
| Feb 16, 2022 at 7:59 | comment | added | winni2k | Also, there has been some recent work on improving imputation speed using very large reference panels: journals.plos.org/plosgenetics/article?id=10.1371/… | |
| Feb 16, 2022 at 7:59 | comment | added | winni2k | If you do want to use the haplotype reference consortium (HRC) panel, then you may need to upload your SNP-chip data to an imputation server, as the HRC panel is partially restricted due to the wishes of the participants. | |
| Feb 15, 2022 at 16:06 | vote | accept | Dan Bolser | ||
| Feb 15, 2022 at 16:06 | comment | added | Dan Bolser | Nice, I didn't know that impute2 did that. Very cool. I take your point that some samples will have better (more extensive and reliable) imputation than others. | |
| Feb 14, 2022 at 21:58 | history | answered | winni2k | CC BY-SA 4.0 |