The Life of Trees
(or: Still Another Phylogeny Program)

SAPP

The CSV-Analysis tool reads STRs and SNPs from a group of downloaded files from Family Tree DNA or Full Genomes Corp to provide better insight into SNPs that may divide the group, and to automate the creation of an input file for the SAPP program.



To use this tool, first download the STR and SNP files for the group you wish to study.



For Family Tree DNA, STRs are produced either by a Y37/Y67/Y111 DNA test, or a NGS test like a Big Y500 or Y700. For Big Y tests for instance, log in to Family Tree DNA under the kit id, and under the "Big Y" section of the Dashboard the STR data can be found under the "Y-STR Results" tab, and the SNP data can be found under "Results".



Example1



From the STR Results page, scroll down to the bottom to find the button to download the STR CSV file.



Example2



From the Results page, the button to download the SNP CSV file is either on the Named Variant or Unnamed Variant tab (NOT the Matching tab which downloads a different CSV file that is not used here).



Example3



If you are a project admin for these kits, you can download the CSV files yourself; otherwise you will need to ask the users to send you their data.



For Full Genomes Corporation, STRs and SNPs are both produced by the particular NGS test taken. The exact file name depends on when the test was taken and which test it was, but in general STR data can be found in the YSTR folder and SNP data in the YSNP folder of the downloaded files from FGC. To use, copy the files from those two folders that match any of the file names shown below into a separate folder along with any other Family Tree DNA or Full Genomes Corp files you wish to run. Note that not all of these files will exist! Some are created by older FGC tests, some by newer.



Example4



If there are several .out files in the YSTR folder, please be sure to take the one marked 'ftdna', NOT any others.



Please do not rename any of these files since the program depends on the filenames.



Once you have these files downloaded into a folder, go to the CSV-Analysis tool, press the button to select files, and select/highlight the STRs and SNP files you want to analyze together.



From the STR Results page, scroll down to the bottom to find the button to download the STR CSV file.



There are two additional checkboxes to select program options:

1) The "Report Only SNPs in Quality Regions" checkbox (if checked) limits reporting to only include SNPs within the Poznik, McDonald, or CombBed regions. Otherwise reporting will include SNPs which are not in any of these regions.

2) The "Report Only SNPs Found In All Tests" checkbox (if checked) limits reporting to only those SNPs which have a positive or negative status for all kits in the group. Otherwise reporting will include SNPs which are positive or negative in some kits and no-calls (unknown) in others in the group.

Inputs (CSV Analysis)