I'm not certain if this is pertinent to the question of calling and the "..." disclaimer mentioned, but one of the projects that have involved me in their analytical work has been having a time with no calls and what they believe are bad calls coming out of Geno2 which is the same technology as the Chromo2 chip. There seems disparity between the raw data down loaded and the calls or no calls presented in the transferred to FTDNA SNP report. I am not really involved in the argument between this project and FTDNA because it is their administrator and members dilemma, but they have involved me by keeping me abreast of the progress and/or lack there of in resolving the situation. I have seen the files and understand what the complaint is about. I'm wondering if indeed there is a similarity here with further question as to interpretation then of what the calls are actually, ie the disclaimer and then further interpretation by the geneticists reviewing Chromo2. I don't have an opinion as I'm certainly not qualified to have one, but...there is a question here me thinks. Susan Hedeen On 11/16/2013 10:13 AM, Iain Kennedy wrote: > Walter, > > I quoted the S SNPs exactly as they appear, I'm sure you know with your knowledge that you can look these all up on the ISOGG tree - for the benefit of others I posted the link the other day: > > http://www.isogg.org/tree/ISOGG_HapgrpR.html > > I am happy to analyse peoples files for them if they don't want the fiddle, on the other hand if you are going to dive in then you may as well familiarise yourself with some of the alternative names. Not an issue for the sub-M222 SNPs apart from the well known S675=DF85. > > The total number of SNP data rows in mine is 14173, ditto Robert McBride's. > > Wasn't there a similar issue with the call values in some Geno files? Anyway there is some text at the start of the file which reads thus: > > "A small number of markers give apparent heterozygote calls, e.g. AG. As shown in the result column, these indicate a positive call. The reason they appear to be heterozygous is again because of limitations in the Illumina clustering software, which expects three clusters. If the true positive and negative clusters are too close together, it is not possible to force a homozygous call for the one variant, hence an AG call is allowed. Our downstream scripts register this as a positive call." > > regards > > Iain > > > > > >> Date: Sat, 16 Nov 2013 08:04:59 -0500 >> From: [email protected] >> To: [email protected] >> Subject: Re: [R-M222] Chromo2 Raw Results s588 >> >> Thanks, Iain. >> >> I must have missed your 16 Oct post on the Chromo2 raw file format, or >> rather was not in the frame of mind at that moment to adsorb that bit of >> information. >> >> I do remember some discussion on this list of form issues with the >> Chromo2 data and perhaps a bit of an air of disappointment that the data >> (if as represented below) is not more like what we are used to seeing in >> a raw file format from 23andMe or FTDNA where there is a reference to >> the chain position of a SNP and possibly a human genome reference >> sequence number as well as the SNP call. >> >> "S" designations as you show below are not particularly enlightening, >> possibly because of lack of familiarity with them on my part. To >> paraphrase, "A SNP by any other name is still a SNP," I suppose except >> that since much of this is more abstract than your basic rose, it is a >> bit harder to understand. >> >> In the data below, I suppose I am puzzled by the heterozygous calls of >> S116 and S474. Since there is only one DNA strand and not two, unlike >> for chromosomes in the autosome, I can understand the homozygous calls >> for the remaining SNPs shown below as being double letters owing to chip >> read software programming etc. But why "AC" and why "AG" for S116 and S474? >> >> And a further question: How many lines (or SNP calls) of text in the >> Chromo2 raw file? Tens? Hundreds? Thousands? >> >> Walter >> >> On 11/16/2013 4:30 AM, Iain Kennedy wrote: >>> For those who want to look at their SNP hierarchy it should look like this in part: >>> >>> S116 AC positive >>> S145 GG positive >>> S474 AG positive >>> S193 AA positive >>> Z2961 AA positive >>> >>> and then the SNPs in the Wilson tree/diagram. However note that you will not see M222 itself: there may be an equivalent or closeby SNP but Dr. Wilson is still double checking this. >>> >>> Iain >>> >>> From: [email protected] >>> To: [email protected] >>> Date: Sat, 16 Nov 2013 07:13:35 +0000 >>> Subject: Re: [R-M222] Chromo2 Raw Results s588 >>> >>> Walter, >>> >>> If you ordered the raw version you can download a .txt file whose format I described last month in this post: >>> >>> http://archiver.rootsweb.ancestry.com/th/read/DNA-R1B1C7/2013-10/1381923024 >>> >>> and that is what we examine. You get it by logging in to your account and clicking the Download button. I can't say for sure that Steve has a downloadable file (yet). If he doesn't he can email [email protected] and they should be able to send it him. >>> >>> Iain >>> >> >> ------------------------------- >> To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message > > > ------------------------------- > To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message >