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  • $\begingroup$ 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. $\endgroup$
    – Dan Bolser
    Commented Feb 15, 2022 at 16:06
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    $\begingroup$ 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. $\endgroup$
    – winni2k
    Commented Feb 16, 2022 at 7:59
  • $\begingroup$ Also, there has been some recent work on improving imputation speed using very large reference panels: journals.plos.org/plosgenetics/article?id=10.1371/… $\endgroup$
    – winni2k
    Commented Feb 16, 2022 at 7:59
  • $\begingroup$ 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). $\endgroup$
    – Dan Bolser
    Commented Feb 16, 2022 at 16:14
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    $\begingroup$ 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#! $\endgroup$
    – winni2k
    Commented Feb 16, 2022 at 19:47