Convert Illumina Human Hapmap 550 K Chip Manifest File From B36 To B37

Question

[Kevin]

Hi I have old data that was genotyped on convert Illumina Human Hapmap 550 k chip the old manifest file is in b36. What's the best way to migrate this info to b37?

I know one approach was to use bwa to align the probes and annotating the sam file. But I googled and can't find a tool that does this . Just checking if there's already an avail pipeline out there ( I mean Illumina probably needs to do this for their own chips, they provide liftover files for the ones that they did )

Answer 1

[Istvan Albert]

There is no single best way to do this type of transformations. There are many unexpected complexities that arise - hence the lack of support from the company as well (not to mention that there is no financial incentive).

I personally think that the proper way to deal with a situation like this is to merge the results of the analysis not the data itself. Think of if as a replicate analysis, can your old data with the old annotation produce the same or similar outcomes as the new data and new annotations.