Auxiliary data for the H3Agwas workflow :

Strand data for the H3A Chip Manifest 3

This data is provided without any other warranty than this is what we used to do alignment against the GrCh 37 build.

The h3a_A3.ref file can be used as the "reference" parameter for the work flow. It contains the base of the + strand of the Build 37 reference genome at each position of the chip. Please note that there are two other files

Note that all the SNPs in the warning and error files are in the reference file with the base as specified by the reference genome. It is up to you to decide later whether to include or exclude them.

Suggested reading

I recommend the following paper to understand alignment