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Help! Gedmatch upload - No-calls = 31101

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  • Help! Gedmatch upload - No-calls = 31101

    Hi,

    I uploaded my raw data (36) to gedmatch and did a diagnostic test om my data.

    Do I have to reupload my FTDNA Familyfinder raw data?



    Kit T901755 was uploaded on 2017-12-17 16:00:49 (GMT / UTC)
    Kit was tokenized on 2017-12-17 16:01:19 (GMT / UTC)

    No-calls = 31101 = 4.3779499184264 percent.

    This kit has an unusually high number of no-calls, which usually results in a larger number of false matches.

  • #2
    The number of no-calls has nothing to do with how you uploaded your DNA data file. Uploading it again will produce the same result. It would be interesting to know if FTDNA thinks your Family Finder kit has an unusual number of no-calls, and whether they would be willing to rerun the test in order to improve your results.

    I'm also interested to see that GEDmatch equates excessive no-calls with the occurrence of false matches. I have long suspected something like that, if it tends to occur more often in particular chromosome segments, might account for several groups of weak matches that can't be resolved into "maternal" and "paternal" sets.

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    • #3
      John,

      Thank you for your answer. I will let FTDNA know of my the amount of no calls as it is as high as 4.4%

      Hopely they can rerun my Familyfinder,

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      • #4
        Like everybody else submitting recent (mid-2019) FTDNA kits to GEDmatch and running their diagnostic utility, I'm also getting that 30,000 / 4% no-calls.

        Discussed elsewhere on the Internet, it seems that FTDNA added/removed 30,000 somethings, and has just empty filler there(?) So my beginner question would be if the length of those somethings is less than 7cM, would it matter?

        Since the staff is not answering this on these forums, I've submitted a request ticket for the two kits I manage. And I would hope they address this issue in their FAQs, as many of us are wondering if we got a bum kit, or if they have a bum chip, or anything else that would have caused a bad analysis.

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        • #5
          Pretty sure "no-calls" are not counted as mismatches by GEDmatch, so the effect should be minimal, unless perhaps the no-calls happen to be concentrated in some particular region, thus having a disproportionate effect on the number of SNP's available for comparison within that segment. The effect of comparing, say, an Ancestry kit with a kit from FTDNA should be much more significant (because the total number of SNP's that are scored in both kits will be even lower), and we still manage to find and analyze matches of all sizes from such comparisons.

          That said, it is NOT HELPFUL for FTDNA to leave a placeholder in the raw data file for SNP's that is has actually given up on scoring (if that is actually what is happening), because such a practice interferes with the assessment of the quality of the data.

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          • #6
            If I recall, in the old days FTDNA would tolerate only a couple of a percent and most kits had less than a half percent.


            Jack

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            • #7
              That's what I remember too -- but if the information in this thread is correct, they seem to be claiming now that the extra 30,000 "no-calls" don't count, because they are no longer scoring those SNP's. There are certainly better, clearer ways to present data.

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              • #8
                Originally posted by rd298935 View Post
                Like everybody else submitting recent (mid-2019) FTDNA kits to GEDmatch and running their diagnostic utility, I'm also getting that 30,000 / 4% no-calls.

                Discussed elsewhere on the Internet, it seems that FTDNA added/removed 30,000 somethings, and has just empty filler there(?) So my beginner question would be if the length of those somethings is less than 7cM, would it matter?

                Since the staff is not answering this on these forums, I've submitted a request ticket for the two kits I manage. And I would hope they address this issue in their FAQs, as many of us are wondering if we got a bum kit, or if they have a bum chip, or anything else that would have caused a bad analysis.
                Hmm, I'd been assuming that the no-calls were randomly distributed. Could I ask you to compare the no-call locations for the kits you mentioned? If this is tedious for you, you could email me the raw data and I'll check them with an Excel formula. My email is [email protected].

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                • #9
                  Thank you Ann! I was hoping somebody would step up to resolve the question of how the reputed 30,000 unscored SNP's are distributed.

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                  • #10
                    rd298935 kindly sent me the raw data files for himself and his wife.

                    He had 30,613 no-calls and his wife had 32,259. Most of the no-calls in his file (28,281) were also found in his wife. I actually expected less overlap, so it would be interesting to add another file or two to the comparison.

                    The no-calls were pretty evenly distributed over all the chromosomes, ranging from a low of 2.5% for C1 and 5.5% for the X (overall average 4.2%.

                    The maximum number of no-calls for consecutive SNPs was three, so I don't think there will be a big impact on the matching algorithms. No-calls are treated as if they would match, and the algorithm might overlook some genuine mismatches between people. However, other mismatches will crop up sooner or later anyway if there is no true matching segment.

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                    • #11
                      Excellent! Data is always better than no data!

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                      • #12
                        Originally posted by Ann Turner View Post

                        He had 30,613 no-calls and his wife had 32,259. Most of the no-calls in his file (28,281) were also found in his wife.
                        Hmmm. GEDmatch's DNA file diagnostic utility for me reported:
                        No-calls = 28961
                        Number of SNPs utilized by GEDmatch template = 709336
                        Number of regular SNPs = 681626
                        And for my wife:
                        No-calls = 30643
                        Number of SNPs utilized by GEDmatch template = 709336
                        Number of regular SNPs = 679944

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                        • #13
                          My results: No-calls = 942 = 0.13368206091758 percent.
                          My wife's results: No-calls = 2433 = 0.34865474868341 percent.

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                          • #14
                            Meanwhile, my support ticket got the reply that the two kits percentages (4%) are within their "quality control checks and measures."

                            And that:
                            "Some atDNA SNPs which are not included in our test have placeholders in the raw data file for formatting purposes which can inflate a different service's no call calculation."

                            I'm going to ask what that means. In other words, formatted for who?

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                            • #15
                              Originally posted by rd298935 View Post
                              Meanwhile, my support ticket got the reply that the two kits percentages (4%) are within their "quality control checks and measures."

                              And that:
                              "Some atDNA SNPs which are not included in our test have placeholders in the raw data file for formatting purposes which can inflate a different service's no call calculation."

                              I'm going to ask what that means. In other words, formatted for who?
                              This means that if say gedmatch template includes a specific SNP which is say tested in the Ancestry Raw Data but not FTDNA Raw Data, your file (FTDNA Raw Data upload) at Gedmatch, for that SNP will be entered as a no call.

                              Gedmatch only extracts from your Raw Data file the SNPs which they have in their template. Any SNPs not listed in template are discarded, any SNPs in template that are not listed in your raw data file will be entered as no calls.
                              So if the no calls in your file happen to be ones used by template, they will be also entered as no calls at Gedmatch, add to that the no calls entered for any SNP in template that is not tested in your original raw data.
                              Result, the possibility of a higher rate of no calls, if Gedmatch counts these non tested SNPs in their no call percentage.
                              Last edited by prairielad; 9 July 2018, 09:03 PM.

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