Getting Started with SAPP

Beginning training video for SAPP, including both how to gather the STRs for a group of kits and an explanation of the input file formats. The video also includes four examples of how SAPP calculates different trees based on various changes in the input file.

[@kmackey1258]

Thank you so much. All of your videos are great. You have helped so much with my very limited knowledge.

[@DaveVance01]

You're very welcome!

[@earlscottchambers4280]

Initial observation is this may in fact make things most confusing but just using the standard minimum, it may give us a graph of where our SNPs are. I would like to know what does your internal Haplotree structure look like? Can we view your internal tree?

[@DaveVance01]

Earl Scott Chambers What standard minimum do you mean? BTW to see if a SNP is in the internal tree or to see the tree structure, use the “SNPTREE” link at the top of the SAPP webpage, and enter a SNP name there. If that SNP is in the internal database it will draw the tree structure under (downstream from) that SNP.
It’s important to note though that the internal SNP tree is only used to guide SAPP with additional SNP results beyond what was entered in the input file. So for instance if SNP2 is downstream from SNP1, and a kit is marked as SNP2+, SAPP would know from the internal tree that that kit would also be SNP1+. Beyond that kind of “deduction”, SAPP doesn’t use the SNP internal tree.