We would like to take advantage of the latest patch of GRCh38, but we also want to use the no alt analysis set. From the FTP links on the GRC site, I can only see the "analysis_set" versions for the base GRCh38, not the patched versions. Is anybody else using patched no alt (or other analysis set versions)? If so, how are you doing it?
Sidebar: more general question: of all of the versions/flavors avaliable, what are people using?
So far, I've thought of:
1. Downloading the patched version and manually removing sequences I don't want and renaming to chr1, chr2, etc. The problem is that this doesn't get me the same masking as no alt, and I'm concerned of the possibility of doing something differently than the norm, which can cause problems if we're processing BAMs from somewhere else.
2. Create an actual patch file by diffing the base and patched version, and apply that patch to the no alt.
Both of these feel very wrong, and I'm thinking there has to be a best practice (or at least a better one).
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