Since the publication of the article on nomenclature of Y-STR markers by Butler, et al [Journal of Genetic Genealogy, 4:125-148 (2008)], most companies have adopted the recommendations. Therefore, for a Y-STR haplotype reported for a recent test (post-2010), there are probably no nomenclature issues to worry about. The haplotype can simply be entered as is. For haplotypes that are pre-2009, depending on the lab that did the testing and when it was done, there may or may not be some issues to deal with. The material below relates to the situation that pertained prior to the adoption of the industry recommendations published in JoGG.
There may possibly still be a difference in reporting of one repeat on the markers DYS481 and DYS594 as reported by Ethnoancestry between 2007 and 2011. If these markers were tested at Ethnoancestry and used with the Haplogroup Predictor program, please review the information below on these two markers.
Where Y-Search had established a convention for a marker nomenclature, this convention was adopted for the haplogroup prediction program. This includes the 67-marker set now offered by FTDNA. However, in some cases of markers that FTDNA does not test, Y-Search has not established a convention. In such cases, the NIST conventions have been adopted where they can be determined. NIST has been asked to settle some of these nomenclature issues and when this happens, the haplogroup program will be adjusted to the NIST standards [Note: The NIST recommendations have now been published--see above]. Note that the reading of the standards published by the International Society of Forensic Genetics (supported by NIST) by Sorenson Genomics is apparently not the same as read by others.
If you tested with Sorenson Molecular Genealogy Foundation (SMGF), you can set your "lab standard" as FTDNA and all of your values will be automatically adjusted for you as they are reported. No further changes would be necessary. If you use the SMGF (which claims to meet ISFG) standard as your reporting option, then you will need to adjust your values as discussed below.
The data on allele frequencies for the markers DYS485, 495, 505, 508, 522, 532, 533, 540, and 556 [in the pre-2012 versions of the program] came primarily from NIST studies. While no specific standards for these were found, it was presumed that NIST used their own conventions. However, when FTDNA started testing DYS450, they did not follow the lead of NIST and established their own nomenclature. FTDNA reports values that are one less than NIST for DYS450. Until NIST issues their opinion on the disputed marker nomenclature, the FTDNA conventions will be followed.
CAUTION: If you enter marker values for DYS485, 495, 505, 522, 532, 533, 540, 556, or 643, many of the haplogroups will drop out of the probability calculation (for lack of data from those haplogroups) and the marker box will turn orange in color. Omit these markers if you wish to see probabilities for all of the haplogroups. Genetree customers in particular should not enter their value of DYS522 if they wish to see the full set of haplogroups used.
The following markers are handled differently by different institutions and companies and values on these markers may need to be adjusted prior to use in the program, depending on who performed the test. Note that when extracting data from the SMGF database, one can select a lab standard, such as FTDNA, and so any values extracted will be on the same basis as values from FTDNA and should not need adjustment for use in this program.
DYS019 - This marker is also known as DYS394. The Sorenson (SMGF) database values were formerly one larger than the conventional value at other labs and at Y-Search. That is, a value of 13 at Y-Search (or FTDNA) becomes a value of 14 at SMGF. However, SMGF now has changed their convention to match that of other labs, and there are apparently no differences between any of the labs. Values taken from the SMGF database now should not need adjustment, but if you recorded your values from SMGF prior to mid-2007, you should probably check the current values.
DYS441 - This marker was formerly scored almost uniformly across the different labs, but in mid-2007, the Sorenson lab changed to a reporting standard that increased the repeat value by one unit, while FTDNA and some others remained the same. The FTDNA standard is used in this program. If you tested with DNAH, Ancestry.com, or SMGF, you need to subtract one unit from your DYS441 value. If you tested with Genebase, you need to add one unit.
DYS442 - This marker was formerly scored almost uniformly across the different labs, but in mid-2007, the Sorenson lab (SMGF, Ancestry.com, DNAH) changed to a reporting standard that increased the repeat value by five units, while FTDNA and most others remained the same. The FTDNA standard is used in this program. If you tested with DNAH, Ancestry.com, or SMGF, you need to subtract five units from your DYS441 value. If you tested with Genebase, DNA Fingerprint, or Relative Genetics, you do not need to adjust your value.
DYS448 - This marker in the SMGF database formerly had a value that was three units larger than those reported by other labs. In this case also, SMGF has now changed their conventions to match other labs, and the same comments apply as above under DYS019.
DYS452 - This marker was formerly reported according to two different standards that differed in repeat count by 19 units. However, it appears that all of the major labs have now standardized on the larger value and this value should be used with this program.
DYS454 - This marker is reported the same by all labs except Genebase. If you tested with Genebase, you need to add one unit to your value for use with this program.
DYS458 - This marker is reported the same by all labs except Genebase. If you tested with Genebase, you need to add two units to your value for use with this program.
DYS461 - It appears that all of the major labs have now standardized on one approach to scoring this marker and this value should be used with this program.
DYS463 - This marker was formerly reported according to two different standards that differed in repeat count by two units. However, it appears that all of the major labs have now standardized on the larger value and this value should be used with this program.
DYS481 - Ethnoancestry reports a value one less than does FTDNA. Add one to your EA value for use in the program.
DYS594 - Ethnoancestry reports a value one less than does FTDNA. Add one to your EA value for use in the program.
GATA-A10 - Values reported by SMGF, Ancestry.com, and DNAH should be reduced by two units before use with this program.
GATA-H4/TAGA-H4 - This marker is also called TAGA-H4 by DNAH, Relative Genetics, and NIST, and called GATA-H4 by FTDNA. When the marker is reported as GATA-H4, its value is one less than when it is reported as TAGA-H4. Y-Search uses GATA-H4 and this will be used by the haplogroup predictor program also. To confuse matters further, Sorenson Genomics (test lab for SMGF, DNAH, Relative Genetics, and others) now reports this marker as 9 units greater than it formerly did, resulting in its values being 10 units larger than those of FTDNA and 9 units larger than those reported by the former company, DNA Fingerprint. The FTDNA standard will continue to be used in this program. For some reason, Ancestry reports this marker as one unit less that does Sorenson Genomics, so the value reported by Ancestry should be reduced by 11 units before use with this program.