Hi Ann, At your suggestion I had another look at the LiftOver function of Genome Browser, https://genome.ucsc.edu/cgi-bin/hgLiftOver and Yes, it works too, and is possibly simpler than my earlier method. Method:- 1.    Start with your list of hg19 SNP positions in any order and place in a spreadsheet starting at cell A1. 2.    Alongside, use the formula =CONCATENATE("chrY:",A1,"-",A1) and copy down the list of SNP positions. 3.    Copy this text list and paste into the input window in the Genome Browser, https://genome.ucsc.edu/cgi-bin/hgLiftOver 4.    Make sure the "Original Assembly" is set to hg19 and "New Assembly" is set to hg38 and press "Submit" 5.    Under 'Results' is a link "View Conversions', click this link. 6.    A file is downloaded to your computer named in the form:- "hglift_genome_70f0-d4f300.bed" 7.    Your results are returned in the same order as submitted in the format "chrY:xxxxxxxx-xxxxxxxx" 8.    Use the formula =ABS(RIGHT(A1,8) to return the hg38 position Hope this helps* * *Dennis Wright* On 10/10/2017 11:14 PM, Ann Turner wrote: > I received a note off-list reminding me about the LiftOver tool at the UCSC > Genome Browser website: > > https://genome.ucsc.edu/cgi-bin/hgLiftOver > > There has been some discussion on the mailing list for the ISOGG tree about > whether there are some "gotchas" in that method, though. Dennis, could you > review that method and see if it comes up with the same results? > > Ann Turner > > On Tue, Oct 10, 2017 at 4:06 AM, Ann Turner <[email protected]> wrote: > >> For step 3, do you mean that you (as a human being) are scanning the >> adjustment table and doing a copy-and-paste? It seems like there could be >> some formulas to automate that. >> >> Ann Turner >> >> On Tue, Oct 10, 2017 at 12:55 AM, Dennis Wright <[email protected]> >> wrote: >> >>> For those that have a spreadsheet with a large number of SNPs presently >>> showing hg19 positions, you are probably wondering what is involved in >>> producing hg38 positions. Here is how I went about it. >>> >>> I have been able to organise my SNP positions with the help of the >>> mutation page produced by Alex Williamson, http://www.ytree.net/hg19tohg3 >>> 8.html. >>> >>> 1. I took the list of my 695 SNPs and pasted the hg19 positions into >>> column A of a new spreadsheet. >>> >>> 2. Copy this list into Column D >>> >>> 2. Sort Column D from smallest to largest >>> >>> 3. In column E insert the adjustment specified in Alex's listing. As >>> these are ranges, copying in the adjustments is quite quick, and this is >>> the worst part of the whole procedure. >>> >>> 4. Calculate the new position in column F with a formula that adds or >>> subtracts column E from column D as appropriate. >>> >>> 5. In column B, Cell B1, insert the formula =VLOOKUP(A1,D:F, 3,FALSE) >>> and copy this formula to the bottom of your list of positions. >>> >>> 6. Column B now holds the hg38 positions of your SNPs in the order of >>> your original list. Copy this Column, >>> >>> 7. 'Paste Special' choosing 'Values' to your original SNP listing >>> spreadsheet and job is done! >>> >>> I hope this helps others do their conversions (Thanks Alex) >>> >>> Kind regards all! >>> >>> *Dennis Wright* >>> Donnchadh Mac an tSaoir >>> Irish Type III R-L226 > FGC12290 >>> /"We are merely the present-day custodians of our Ancestors genes." >>> >>> >>> / >>> >>> On 10/10/2017 9:09 AM, McDonald, J Douglas wrote: >>> >>>> I got a reply to a question about this. Its pretty clear. >>>> >>>> It says: >>>> >>>> >>>> "Remapped vcf and BED files will be generated from the remapped BAM >>>> files, though it may take a few days after the re-run is complete for them >>>> to be available. >>>> >>>> A remapped downloadable BAM file will be available on request at some >>>> point after the re-run. We do not yet know when that will be. >>>> Those who have a hg19 BAM file will have to request a hg38 BAM file. We >>>> won't automatically replace them. " >>>> >>>> That means that all the raw data, if you re-download all of it, will be >>>> coherent. This is very good news >>>> if its accurate. >>>> >>>> Doug McDonald >>>> ________________________________________ >>>> From: GENEALOGY-DNA >>>> Dear All, >>>> >>>> Earlier today I received an e-mail from FTDNA that they will be moving >>>> from >>>> Build 37 to Build 38 for the BigY. >>>> ------------------------------- >>>> 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 >>> >> > > ------------------------------- > 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 >

I'm glad to hear that worked. I gather the results were consistent with your other method? Ann Turner On Tue, Oct 10, 2017 at 5:13 PM, Dennis Wright <[email protected]> wrote: > Hi Ann, > > At your suggestion I had another look at the LiftOver function of Genome > Browser, https://genome.ucsc.edu/cgi-bin/hgLiftOver and Yes, it works > too, and is possibly simpler than my earlier method. > > Method:- > > 1. Start with your list of hg19 SNP positions in any order and place in > a spreadsheet starting at cell A1. > > 2. Alongside, use the formula =CONCATENATE("chrY:",A1,"-",A1) and copy > down the list of SNP positions. > > 3. Copy this text list and paste into the input window in the Genome > Browser, https://genome.ucsc.edu/cgi-bin/hgLiftOver > > 4. Make sure the "Original Assembly" is set to hg19 and "New Assembly" > is set to hg38 and press "Submit" > > 5. Under 'Results' is a link "View Conversions', click this link. > > 6. A file is downloaded to your computer named in the form:- > "hglift_genome_70f0-d4f300.bed" > > 7. Your results are returned in the same order as submitted in the > format "chrY:xxxxxxxx-xxxxxxxx" > > > > 8. Use the formula =ABS(RIGHT(A1,8) to return the hg38 position > > Hope this helps* > * > > *Dennis Wright* > > > > > > On 10/10/2017 11:14 PM, Ann Turner wrote: > >> I received a note off-list reminding me about the LiftOver tool at the >> UCSC >> Genome Browser website: >> >> https://genome.ucsc.edu/cgi-bin/hgLiftOver >> >> There has been some discussion on the mailing list for the ISOGG tree >> about >> whether there are some "gotchas" in that method, though. Dennis, could you >> review that method and see if it comes up with the same results? >> >