Comments (1)
lemieuxl
commented on June 9, 2024
These are unimportant error messages. There are steps used to check the strands of the markers (i.e. check the alignment of the source dataset with the imputation reference files).
The first step checks the alignment and creates the files chr*.alignments.*. Then, using those files, we flip the markers with alignment problems and recheck the alignment (creating the files chr*.to_exclude.alignments.*. The markers found to have alignment problems are then excluded from the source dataset.
Those "error" messages should not appear in the phasing steps (files chr*.final.phased.log).
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