description of expected out files

[tvkent]

should probably say in the wiki or something what output files you should expect for each analysis and what they're good for. that was a big annoyance for me learning angsd.
also if you run a few analyses, some output names are the same and could overwrite--either make outfile names specific (which could cause problems with cross-compatibility) or put a warning somewhere.

[arundurvasula]

That's a good call. We should explicitly say what files should be used as input for graphing as well.

So each script should have a wiki page with:

• inputs needed
  • bams
  • other prerequisites (as in the case of Thetas and Fst)
• names and functions of output files
  • which files to graph
  • which files go to other analyses
• variables that you need in order to run the analysis
• variables that you can override by providing in the config files

Anything else @rossibarra ?

[arundurvasula]

@tvkent which pages are complete on this?

[tvkent]

ABBA_BABA, FASTA, GL, and THETAS need to be finished by someone who knows the outputs. they're already set up. I think thetas just needs to be checked if it's still piggybacked, bc i think it looks like sfs is included in it now...which it probably shouldn't be in case the user decides to do thetas at a later date on an old sfs file...

[tvkent]

jk thetas is fine

[arundurvasula]

Fixed ABBABABA. Thetas also looks fine

[arundurvasula]

I updated PCA, but I need to change the optional variables.