Changes

==== NCBI build 36 / NCBI build 37 ====

==== NCBI build 36 / NCBI build 37 ====

The 1000G June reference panel is on build 36, future 1000G reference panels will be on build 37. This has also some impact on the pre-phasing:

The 1000G June reference panel is on build 36, future 1000G reference panels will be on build 37. This has also some impact on the pre-phasing:

your data must be on the corresponding build, or in other words, all SNPs must be ordered correctly based on the used build. Therefore, if you want to use your pre-phased data to impute into NCBI build 36 and NCBI build 37 reference panels, you have to exclude all SNPs that change order between builds.

some SNPs will ordered differently in each genome build (we expect order will be more accurate in more recent builds!). Purists will claim that imputation using NCBI build 36 and NCBI build 37 reference panels requires phasing using the exact same reference panel -- others will claim this makes little difference.

 

 

Here we will provide exclusions list for various genotyping platforms:

* [http://www.sph.umich.edu/csg/cfuchsb/metab_order_changed.txt Metabo-Chip]

=== Running MaCH ===

=== Running MaCH ===