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If figuring out position and strand for each marker seems like hard work, don't despair. For you, this should be the hardest bit of the entire process! For the computer, the fun is about to start.
If figuring out position and strand for each marker seems like hard work, don't despair. For you, this should be the hardest bit of the entire process! For the computer, the fun is about to start.
==== 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:
your data must be on the correct 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 build 36 and build 37 reference panels, you have to exclude all SNPs that change order between builds (MaCH does not use genomic coordinates).
Here we will provide exclusions list for various genotyping platforms:
Metabo-Chip
=== Running MaCH ===
=== Running MaCH ===
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