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Thread: BigY move to hg38

  1. #21
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    Quote Originally Posted by rms2 View Post
    I saw that when I did a search a little while ago, but apparently I lack the prerequisite knowledge to use it. I was hoping for something that would give me a quick conversion for a single position in HG38, in this case 11333103, back to the equivalent position in HG19.
    Hg38 11333103 maps back to Hg19 13488779. However it is also present in the VCF files of my S841 group, sub group of Z253. And looking at the Hg19 BAM results it’s garbage with multiple Variants in the same read sequence. I’m seeing a lot of this type of result in the Hg38 reports in my group, and some of them have been given BY labels.
    Last edited by Muircheartaigh; 11-05-2017 at 02:45 PM.

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  3. #22
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    Quote Originally Posted by rms2 View Post
    I saw that when I did a search a little while ago, but apparently I lack the prerequisite knowledge to use it. I was hoping for something that would give me a quick conversion for a single position in HG38, in this case 11333103, back to the equivalent position in HG19.
    Just enter chrY:11333103-11333103 in the box labelled Paste in data and click Submit. Then double click where it says View conversions below.
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019, FGC-10X Linked Reads Apr 2019, Dante-Nanopore May 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
    Hidden Content
    FBIMatch: A828783 (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

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  5. #23
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    Quote Originally Posted by MacUalraig View Post
    Just enter chrY:11333103-11333103 in the box labelled Paste in data and click Submit. Then double click where it says View conversions below.
    Ah. I tried that but minus "chrY:" and the dash. Thanks. I'll give it another shot.
     


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    Y-DNA: R1b-FGC36981 (L21> DF13> Z39589> CTS2501> Z43690> Y8426> BY160> FGC36974>FGC36982 >FGC36981)

    Additional Data:
    Lactase Persistent:
    rs4988235 AA (13910 TT)
    rs182549 TT (22018 AA)

    Red Hair Carrier:
    Arg160Trp+ (rs1805008 T) aka R160W

    Dad's mtDNA: K1a1

  6. #24
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    Quote Originally Posted by rms2 View Post
    I saw that when I did a search a little while ago, but apparently I lack the prerequisite knowledge to use it. I was hoping for something that would give me a quick conversion for a single position in HG38, in this case 11333103, back to the equivalent position in HG19.
    For a simple conversion try the NCBI Genome remapping service. You can input single locations, copy paste or upload files using the format Y.xxxxx-xxxxx in your case choose GrCh38(Hg38) as the source assembly and GrCh37(Hg19) as the target assembly and type Y.11333103-11333103 into the Data panel and submit
    Last edited by Muircheartaigh; 11-05-2017 at 02:48 PM.

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  8. #25
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    Quote Originally Posted by Muircheartaigh View Post
    Hg38 11333103 maps back to Hg19 13488779. However it is also present in the VCF files of my S841 group, sub group of Z253. And looking at the Hg19 BAM results it’s garbage with multiple Variants in the same read sequence. I’m seeing a lot of this type of result in the Hg38 reports in my group, and some of them have been given BY labels.
    Thanks. Too bad. I was hoping this would be some new info that would be supported once the other guy with my terminal SNP (FGC36982) gets his updated Big Y results.
     


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    Y-DNA: R1b-FGC36981 (L21> DF13> Z39589> CTS2501> Z43690> Y8426> BY160> FGC36974>FGC36982 >FGC36981)

    Additional Data:
    Lactase Persistent:
    rs4988235 AA (13910 TT)
    rs182549 TT (22018 AA)

    Red Hair Carrier:
    Arg160Trp+ (rs1805008 T) aka R160W

    Dad's mtDNA: K1a1

  9. #26
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    Quote Originally Posted by rms2 View Post
    Thanks. Too bad. I was hoping this would be some new info that would be supported once the other guy with my terminal SNP (FGC36982) gets his updated Big Y results.
    Here's an extract from the VCF file of a member of the S841 group that includes the location of BY26207 showing the reported values in the vicinity of the so called SNP IN question. This sort of garbage is appearing in some of the Hg38 results of members of my group and this is just the tip of the Iceberg. Two Members who share a common ancestor estimated at about 600 years ago have had their private SNPs increased from 5 in the Hg19 build to more than 20 in the Hg38 build. What is strange is that some of these garbage variants are being assigned ''BY'' labels.


    11333005 A G,T
    11333007 G C
    11333009 G A
    11333013 G A
    11333028 T C
    11333029 C A
    11333032 G A
    11333033 T G
    11333037 G A
    11333054 A G
    11333057 G A
    11333062 G A
    11333067 C T
    11333071 A G
    11333079 C T
    11333081 C T
    11333096 G T
    11333103 C G BY26207
    11333116 C G
    11333118 C A,G
    11333119 G T
    11333122 C A
    11333128 C A
    11333130 G A
    11333131 G A
    11333139 C G
    11333140 G T
    11333141 G T
    11333143 C A,T
    11333146 G C,A
    11333152 T C
    11333156 A T
    11333157 G T
    11333164 G A
    11333166 T G
    11333167 T C
    11333168 G C
    11333173 C T
    11333174 G A
    11333175 C T,A,G
    11333176 G A
    11333177 G T
    11333179 G C
    11333180 G A
    11333186 C T
    11333187 C A
    11333189 G T
    11333194 C T
    11333195 G A,T,C

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  11. #27
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    Quote Originally Posted by Muircheartaigh View Post
    Here's an extract from the VCF file of a member of the S841 group that includes the location of BY26207 showing the reported values in the vicinity of the so called SNP IN question. This sort of garbage is appearing in some of the Hg38 results of members of my group and this is just the tip of the Iceberg. Two Members who share a common ancestor estimated at about 600 years ago have had their private SNPs increased from 5 in the Hg19 build to more than 20 in the Hg38 build. What is strange is that some of these garbage variants are being assigned ''BY'' labels.


    11333005 A G,T
    11333007 G C
    11333009 G A
    11333013 G A
    11333028 T C
    11333029 C A
    11333032 G A
    11333033 T G
    11333037 G A
    11333054 A G
    11333057 G A
    11333062 G A
    11333067 C T
    11333071 A G
    11333079 C T
    11333081 C T
    11333096 G T
    11333103 C G BY26207
    11333116 C G
    11333118 C A,G
    11333119 G T
    11333122 C A
    11333128 C A
    11333130 G A
    11333131 G A
    11333139 C G
    11333140 G T
    11333141 G T
    11333143 C A,T
    11333146 G C,A
    11333152 T C
    11333156 A T
    11333157 G T
    11333164 G A
    11333166 T G
    11333167 T C
    11333168 G C
    11333173 C T
    11333174 G A
    11333175 C T,A,G
    11333176 G A
    11333177 G T
    11333179 G C
    11333180 G A
    11333186 C T
    11333187 C A
    11333189 G T
    11333194 C T
    11333195 G A,T,C
    All of us should be entering support tickets to FTDNA requesting that they stop naming inconsistent variants and PLEASE remove them from individuals lists of novel SNPs. They are creating the same type of mess as the original BigY analysis except it is worse with these automatic BY names being applied.

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  13. #28
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    Could it be some project admins are behind the rush to name unreliable variants? I don't mean they are picking unreliable SNPs on purpose, but in their excitement to get SNPs named perhaps they aren't being careful enough?
     


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    Y-DNA: R1b-FGC36981 (L21> DF13> Z39589> CTS2501> Z43690> Y8426> BY160> FGC36974>FGC36982 >FGC36981)

    Additional Data:
    Lactase Persistent:
    rs4988235 AA (13910 TT)
    rs182549 TT (22018 AA)

    Red Hair Carrier:
    Arg160Trp+ (rs1805008 T) aka R160W

    Dad's mtDNA: K1a1

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     Celt_?? (11-18-2017)

  15. #29
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    Quote Originally Posted by rms2 View Post
    Could it be some project admins are behind the rush to name unreliable variants? I don't mean they are picking unreliable SNPs on purpose, but in their excitement to get SNPs named perhaps they aren't being careful enough?
    Unlikely, this is a list from one of my group members' Known SNPS. The vast majority are garbage consecutively labelled from multiple variant sequences and I don't believe that any Admin, or anyone else for that matter would suggest labelling them as Valid. Obviously computer generated based in mis-aligned reads. Three of them are valid SNPs labelled just prior to the Hg19 to Hg38 upgrade.


    BY26040 Yes (+) Yes G A High
    BY26041 Yes (+) Yes C G High
    BY26042 Yes (+) Yes C T High
    BY26043 Yes (+) Yes C T High
    BY26044 Yes (+) Yes C G High
    BY26045 Yes (+) Yes T G High
    BY26062 Yes (+) Yes G A High
    BY26063 Yes (+) Yes A T High
    BY26065 Yes (+) Yes T C High
    BY26067 Yes (+) Yes T C High
    BY26068 Yes (+) Yes G A High
    BY26072 Yes (+) Yes T A High
    BY26073 Yes (+) Yes G A High
    BY26074 Yes (+) Yes T C High
    BY26075 Yes (+) Yes G C High
    BY26079 Yes (+) Yes A C High
    BY26083 Yes (+) Yes C T High
    BY26086 Yes (+) Yes A G High
    BY26088 Yes (+) Yes T C High
    BY26093 Yes (+) Yes T C High
    BY26094 Yes (+) Yes C T High
    BY26095 Yes (+) Yes G C High
    BY26102 Yes (+) Yes T C High
    BY26103 Yes (+) Yes T C High
    BY26105 Yes (+) Yes T C High
    BY26109 Yes (+) Yes C G High
    BY26110 Yes (+) Yes T G High
    BY26111 Yes (+) Yes A G High
    BY26118 Yes (+) Yes A G High
    BY26119 Yes (+) Yes T C High
    BY26120 Yes (+) Yes G A High
    BY26121 Yes (+) Yes T C High
    BY26143 Yes (+) Yes A T High
    BY26157 Yes (+) Yes G A High
    BY26158 Yes (+) Yes A C High
    BY26159 Yes (+) Yes A T High
    BY26160 Yes (+) Yes T C High
    BY26161 Yes (+) Yes T A High
    BY26162 Yes (+) Yes C G High
    BY26163 Yes (+) Yes G A High
    BY26228 Yes (+) Yes T G High
    BY26282 Yes (+) Yes C T High
    BY26364 Yes (+) Yes A G High
    BY26365 Yes (+) Yes G A High
    BY26382 Yes (+) Yes A G High
    BY26383 Yes (+) Yes G C High
    BY26493 Yes (+) Yes A C High
    BY26494 Yes (+) Yes A C High
    BY26495 Yes (+) Yes T G High
    BY26501 Yes (+) Yes C T High
    BY26502 Yes (+) Yes G A High
    BY26503 Yes (+) Yes C G High
    BY26504 Yes (+) Yes A T High
    BY26716 Yes (+) Yes C A High
    BY26720 Yes (+) Yes T C High
    BY26721 Yes (+) Yes A G High
    BY26723 Yes (+) Yes G C High
    BY26725 Yes (+) Yes A T High
    BY26727 Yes (+) Yes A C High
    BY26729 Yes (+) Yes T G High
    BY26730 Yes (+) Yes C A High
    BY26731 Yes (+) Yes C T High
    BY26732 Yes (+) Yes T C High
    BY26734 Yes (+) Yes T C High
    BY26735 Yes (+) Yes T C High
    BY26750 Yes (+) Yes T G High
    BY26751 Yes (+) Yes T A High
    BY26758 Yes (+) Yes T C High
    BY26760 Yes (+) Yes T G High
    BY26763 Yes (+) Yes C A High
    BY26765 Yes (+) Yes G A High
    BY26789 Yes (+) Yes G A High
    BY26790 Yes (+) Yes A G High
    BY26791 Yes (+) Yes A T High
    BY26799 Yes (+) Yes T C High
    BY26800 Yes (+) Yes G C High
    BY26801 Yes (+) Yes A G High
    BY26803 Yes (+) Yes C T High
    BY26804 Yes (+) Yes G A High
    BY26810 Yes (+) Yes C T High
    BY26811 Yes (+) Yes G C High
    BY26812 Yes (+) Yes T G High
    BY26813 Yes (+) Yes C T High
    BY26814 Yes (+) Yes G C High
    BY26815 Yes (+) Yes T C High
    BY26816 Yes (+) Yes T C High
    BY26818 Yes (+) Yes G C High
    BY26820 Yes (+) Yes T C High
    BY26821 Yes (+) Yes G T High
    BY26823 Yes (+) Yes C T High
    BY26824 Yes (+) Yes C T High
    BY26825 Yes (+) Yes G C High
    BY26826 Yes (+) Yes A C High
    BY26831 Yes (+) Yes G C High
    BY26832 Yes (+) Yes G T High
    BY26833 Yes (+) Yes A C High
    BY26837 Yes (+) Yes A C High
    BY26838 Yes (+) Yes G A High
    BY26840 Yes (+) Yes A C High
    BY26841 Yes (+) Yes C A High
    BY26844 Yes (+) Yes A C High
    BY26845 Yes (+) Yes C A High
    BY26848 Yes (+) Yes T C High
    BY26854 Yes (+) Yes G T High
    BY26863 Yes (+) Yes A G High
    BY26878 Yes (+) Yes G A High
    BY26881 Yes (+) Yes A C High
    BY26900 Yes (+) Yes T G High
    BY26901 Yes (+) Yes G C High
    BY26902 Yes (+) Yes A G High
    BY26903 Yes (+) Yes T C High
    BY26904 Yes (+) Yes A G High
    BY26906 Yes (+) Yes C G High
    BY26910 Yes (+) Yes A G High
    BY26929 Yes (+) Yes T C High
    BY26930 Yes (+) Yes C A High
    BY26957 Yes (+) Yes A C High
    BY26994 Yes (+) Yes C T High
    BY26996 Yes (+) Yes G C High
    BY27035 Yes (+) Yes T G High
    BY27036 Yes (+) Yes A C High
    BY27115 Yes (+) Yes T G High
    BY27124 Yes (+) Yes C A High
    BY27125 Yes (+) Yes C G High
    BY27126 Yes (+) Yes G C High
    BY27127 Yes (+) Yes G C High
    BY27761 Yes (+) Yes A A High
    BY27889 Yes (+) Yes T A High
    BY28646 Yes (+) Yes C A High (VALID SNP)
    BY28647 Yes (+) Yes G C High (VALID SNP)
    BY28648 Yes (+) Yes A G High (VALID SNP)
    BY28650 Yes (+) Yes G A High
    BY28651 Yes (+) Yes C T High
    BY28652 Yes (+) Yes T A High
    BY28653 Yes (+) Yes G A High
    BY28672 Yes (+) Yes C G High
    BY28673 Yes (+) Yes C T High
    BY28674 Yes (+) Yes A G High
    BY28675 Yes (+) Yes T A High
    BY28682 Yes (+) Yes C T High
    BY28683 Yes (+) Yes A T High
    BY28684 Yes (+) Yes C G High
    BY28687 Yes (+) Yes A G High
    BY28688 Yes (+) Yes A C High
    BY28689 Yes (+) Yes G C High
    BY28690 Yes (+) Yes A G High
    BY28691 Yes (+) Yes T G High
    BY28693 Yes (+) Yes G A High
    BY28695 Yes (+) Yes C A High
    BY28700 Yes (+) Yes A G High
    BY28701 Yes (+) Yes C T High
    BY28702 Yes (+) Yes C A High
    BY28703 Yes (+) Yes C A High
    BY28704 Yes (+) Yes T C High
    BY28705 Yes (+) Yes A G High
    BY28706 Yes (+) Yes C G High
    BY28707 Yes (+) Yes C T High
    BY28708 Yes (+) Yes T G High
    BY28709 Yes (+) Yes C T High
    BY28710 Yes (+) Yes G C High
    BY28711 Yes (+) Yes G C High
    BY28712 Yes (+) Yes C G High
    BY28713 Yes (+) Yes T G High
    BY28716 Yes (+) Yes C T High
    BY28717 Yes (+) Yes C T High
    BY28718 Yes (+) Yes C T High
    BY28719 Yes (+) Yes C T High
    BY28722 Yes (+) Yes G A High
    BY28723 Yes (+) Yes G C High
    BY28726 Yes (+) Yes A T High
    BY28728 Yes (+) Yes C A High
    BY28729 Yes (+) Yes G A High
    BY28730 Yes (+) Yes T A High
    BY28731 Yes (+) Yes T C High
    BY28732 Yes (+) Yes T A High
    BY28734 Yes (+) Yes C G High
    BY28746 Yes (+) Yes G C High
    BY28749 Yes (+) Yes A C High
    BY28753 Yes (+) Yes C G High
    BY28754 Yes (+) Yes G C High
    BY28759 Yes (+) Yes A C High
    BY28761 Yes (+) Yes A G High
    BY28762 Yes (+) Yes G C High
    BY28773 Yes (+) Yes T G High
    BY28780 Yes (+) Yes A C High

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  17. #30
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    I have lost any R-MC21 matches , I have two at l21 and two at DF13 , 0 at Z39589 and 0 at DF41 ?

    L21 R-L21 2
    DF13 R-DF13 2
    Z39589 R-Z39589 0
    DF41 R-DF41 0
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    ---------------------------------------------------
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    MtDNA - Jordan , Woodham Mortimer, Essex, England , c1800
    Misc bloodlines - Cambridgeshire, Somerset, Kent, Hampshire, Staffs, Devon, Cornwall

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