yFull extracts over 400 STR values from the HG19 BigY BAM file. But there are many no calls and some differences in the value obtained from FTDNA's Sanger Sequencing technique for STRs. We aim to look at this further here to understand which STR values are no call, and eventually understand why, and to understand which tend to give differences from FTDNA's first 111 STR markers. An ultimate goal is to provide further out matching than the 111 currently supported and maybe even identify better, additional STRs that would be good candidates to be tested for. Especially in the Ornery STR Matching identified haplogroups.
This study / question was initiated with a post to the U152 Yahoo Group in 13 Jan 2016. The study has not been formally developed into a form ready to gather large amounts of data. We got maybe 10 submissions of data back in 2016 but never went further. This mostly because BigY-700 product order started including the y111 STRs upgrade (instead of separately having to upgrade). And they have an undocumented feature to order the upgrade to y111 for old, original BigY/BigY-500 tests for only $29.
Alex Williamson's yTree is now starting to collect STR data sets in addition to VCF files. yFull has now started collecting STR files as well.
FTDNA is reportedly now, as part of their conversion from HG19 to HG38, doing the STR extraction similar to how yFull has. Hence the name going from BigY-500 to BigY-700 as they now extract 600+ additional beyond the y111 panels. If so, this would open up widely the potential DB available of STR results to compare with and lead to solving the OSM problem by identifying new STRs that are more unique for those haplogroups.
But FTDNA and ((yFull) have labeled these STRs beyond y111 with private labels. And neither has defined them anywhere. There is no apparent overlap as the value sets are so different. See our page on yDNA STR Index for more information.
This study / question was initiated with a post to the U152 Yahoo Group in 13 Jan 2016. The study has not been formally developed into a form ready to gather large amounts of data. We got maybe 10 submissions of data back in 2016 but never went further. This mostly because BigY-700 product order started including the y111 STRs upgrade (instead of separately having to upgrade). And they have an undocumented feature to order the upgrade to y111 for old, original BigY/BigY-500 tests for only $29.
Alex Williamson's yTree is now starting to collect STR data sets in addition to VCF files. yFull has now started collecting STR files as well.
FTDNA is reportedly now, as part of their conversion from HG19 to HG38, doing the STR extraction similar to how yFull has. Hence the name going from BigY-500 to BigY-700 as they now extract 600+ additional beyond the y111 panels. If so, this would open up widely the potential DB available of STR results to compare with and lead to solving the OSM problem by identifying new STRs that are more unique for those haplogroups.
But FTDNA and ((yFull) have labeled these STRs beyond y111 with private labels. And neither has defined them anywhere. There is no apparent overlap as the value sets are so different. See our page on yDNA STR Index for more information.
External References
- Brad Larkins' Don't Discard the Y-STR's excellent yDNA testing presentation for mid-level to experienced genetic genealogists with hints as to why some STRs cannot be extracted from BAM files.
- Ad-hoc Y-DNA Warehouse group within Haplogroup-R effort (Alex Williamson, et al).
- Robert Casey's study of yFull called STRs in L226
- Felix Immanuel's y-str.org BAM Analysis Kit which incorporates LobSTR for extracting STR's from BAM files (note: deprecated in 2016 but somewhat brought back by Teepean on Github)
- LobSTR, HipSTR, and GangSTR are among many stand alone tools that can be run on NGS result files to extract STRs