SOP Appendix, provide more detail on list of Reference Chromosomes

[lheisler]

Reference chromosomes can be indicated in the analysis xml. This is not a requirement, one can simply provide the code for the reference genome. I've not included these chromosomes for my current submissions using the egasub tool, but i have included in submissions i had done outside of this tool,

The need to include these is stronger if alignments are against specific chromosomes only,

The appendix lists the Tags and Accessions for each of the reference chromosomes, but using this document it is difficult to know precisely which builds or chromosome these apply to. Aligned sequence data files don't necessarily indicate these accessions.

I'm suggesting that this section of the SOP be expanded to provide a bit more detail so the user does not have to look this up elsewhere. ie. in addition to the accession, also provide the build and chromosome name (or other identifiers)

eg.
CM000663.2 GRCh38 Homo sapiens chromosome 1
(https://www.ncbi.nlm.nih.gov/nuccore/CM000663.2)