References

Reference concerns

I've found many versions of hg38. Some with alternates. Some without. Fixes and patches. By themselves, perhaps not a huge problem. Custom references for custom problems.

However not all versions come with the additions files like a gtf/gff. Even the hg38 "package" downloaded from https://support.illumina.com/sequencing/sequencing_software/igenome.html contains different collections of chromosomes in the fasta sequence and annotation gtf file.

Worthy of a concern?

Should I keep our references "up-to-date" by applying all of these patches and fixes?

Patch hg38 reference? https://hgdownload.soe.ucsc.edu/gbdb/hg38/