---------- Forwarded message ----------
From: "Jonathan Marchini" <marchini@ 2013 4:51 PM
Subject: [OXSTATGEN] new version of IMPUTE2 (v2.3.0)
To: <OXSTATGEN>
Cc:
> Hello,
>
> There is a new version of IMPUTE2 (v2.3.0) on the website:
>
> https://mathgen.stats.ox.ac.uk/impute/impute_v2.html
>
> There are several new features in this version:
>
> - IMPUTE2 now has a streamlined way to combine haplotypes from two reference panels and impute from the merged panel. For example, we have seen good results when merging 1000 Genomes haplotypes with sequenced haplotypes from other cohorts to form a combined reference panel. This feature provides accurate imputation of variants that are specific to each panel while maintaining accuracy at variants that are shared across panels. You can read the details of our approach at https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#merging_panels.
>
> - To make the panel-merging as flexible as possible, we now allow the -k_hap parameter to take separate values for each of two reference panels. In essence, you can specify the number of "useful" haplotypes in each reference panel, then IMPUTE2 will take this information into account when merging the reference panels and imputing genotypes in your study. This feature is described here: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#-k_hap.
>
> - We have added important documentation, such as a detailed description of how IMPUTE2 creates the concordance tables that are printed at the end of most runs: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#concordance_tables.
>
> - We fixed some bugs that were present in v2.2.2:
> -- The program used to throw an error when the -use_prephased_g and -chrX flags were combined; now these options are compatible.
> -- You can get phased imputation output by combining the -use_prephased_g and -phase flags, but previously the phasing of hets in the input file (-known_haps_g) was scrambled in the output; this is now fixed.
> -- Another problem with combining the -use_prephased_g and -phase flags is that Type 3 SNPs (those present in the -known_haps_g file but not the reference panel) were omitted from the output haplotypes; now these SNPs are included in the output by default.
> -- Annotations in the reference legend file (columns 5+) used to be restricted to numeric values, but now the program can handle string values as well. This extends the flexibility of the -filt_rules_l mechanism for run-time filtering of reference variants.
>
> - IMPUTE2 can now be made even more accurate by pre-phasing your study genotypes with SHAPEIT2 [ http://www.shapeit.fr/ ], which combines ideas from SHAPEIT and IMPUTE2 to improve the accuracy and efficiency of haplotype estimation. You can read the SHAPEIT2 article here: http://www.nature.com/nmeth/journal/v10/n1/full/nmeth.2307.html.
>
> - We have redesigned the website to make it easier to navigate.
>
> We are still actively improving some of the new features, and we anticipate making another software release in the next few months. In the meantime, we would be happy to hear your feedback about the new software and website.
>
> Happy imputing and Happy New Year!
>
> Bryan and Jonathan
>
> --
> o__ Jonathan Marchini
> c/ /'_ Department of Statistics, University of Oxford
> (+) \(+) 1 South Parks Road, Oxford, OX1 3TG
>
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