GENEALOGY-DNA-L Archives

Archiver > GENEALOGY-DNA > 2013-09 > 1378385022


From: Jim Smith <>
Subject: Re: [DNA] Y DNA analysis from PGP data?
Date: Thu, 5 Sep 2013 07:43:42 -0500


His site looks interesting but it takes a .bam file and my file is a .cgi.
I've googled a bit and perhaps CGAtools and a map2sam tool might convert. I
don't see a contact link on his site. You don't happen to have contact info
do you?

======
Message: 9
Date: Wed, 4 Sep 2013 12:52:58 -0700
From: "John O'Grady" <>
Subject: Re: [DNA] Y DNA analysis from PGP data?
To: "" <>
Message-ID: <>
Content-Type: text/plain; charset="iso-8859-1"

Jim,

Greg Magoon analyzes the Y chromosomes from 1000 Genomes and Personal
Genome results. His web site is:

www.yfull.com

John O'Grady

>
> Early this year my genome was sequenced as part of the Personal Genome
> project, http://www.personalgenomes.org/ So now I have an over 200MB cgi
> file and am wondering how to put it to good use. Are there tools I could
> use to look for the SNPs below my haplotype R1b1a2a1a1a3a1, R-Z306?
> Thanks,
> Jim Smith


On Wed, Sep 4, 2013 at 5:45 PM, <> wrote:

>
>
> Today's Topics:
>
> 1. Re: Thomas Krahn and the Malfunctioning Parts of the FTDNA
> Website (Nelda Percival)
> 2. Re: A Sad Event for Genetic Genealogy (Rex Johnson)
> 3. Re: A Sad Event for Genetic Genealogy (Marleen Van Horne)
> 4. Gok4 ancient Scandinavian farmer and modern European
> variation (Anders P?lsen)
> 5. Ire8 ancient Gotland hunter gatherer and European modern
> variation (Anders P?lsen)
> 6. Ajv70 ancient Gotland hunter gatherer and European modern
> variation (Anders P?lsen)
> 7. Ajv52 ancient Gotland hunter gatherer and European modern
> variation (Anders P?lsen)
> 8. Gene by Gene launches Free My Genes Site (Rebekah Adele Canada)
> 9. Re: Y DNA analysis from PGP data? (John O'Grady)
> 10. Re: A Sad Event for Genetic Genealogy (Itai Perez)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 4 Sep 2013 12:33:07 -0500
> From: Nelda Percival <>
> Subject: Re: [DNA] Thomas Krahn and the Malfunctioning Parts of the
> FTDNA Website
> To: "" <>
> Message-ID: <>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Silvia,
> I have delt with Thomas since he was working his own company, DNA
> FingerPrint. What you just suggested is an insult to the integrity of the
> Krahns.
> I would stake my life on this, the Krahns would never do such a thing or
> be involved in such action.
>
> Nelda Percival Y-dna project admin.
>
> http://www.the-reason-is-love.com This website was created to gather
> information on Shelters, Groups, and Individuals who work to support
> abandoned and abused animals in Europe. Giving you a central location to
> locate a group you would like to work with. Most countries in Europe have
> laws to protect animals but quite a few have no enforcement due mostly to
> graft. If your interested in helping support the homeless animals, please
> visit my website.
>
> Date: Wed, 4 Sep 2013 06:19:25 -0500
> Subject: Thomas Krahn and the Malfunctioning Parts of the FTDNA Website
> From:
> To:
>
> Hello,
>
> Is everyone sure that this is not a case of a disgruntled employee
> sabotaging the parts of the FTDNA website to which he had access and then
> starting a slander campaign against his employers? Was Thomas terminated or
> did he resign without notice? Does someone have a copy of the termination
> letter?
>
> Silvia
>
> ------------------------------
>
> Message: 2
> Date: Wed, 04 Sep 2013 18:56:27 +0100
> From: Rex Johnson <>
> Subject: Re: [DNA] A Sad Event for Genetic Genealogy
> To:
> Message-ID: <>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> I was a DNA-Fingerprint user [along with Ethnoancestry and DNA Heritage]
> before I bought into ftdna testing - when Thomas and Astrid joined the
> organisation. This episode is sad indeed for Thomas, who has always been
> a 'star' in my books.
> What a loss for ftdna this is. What a staggering dent in their credibility.
> I sincerely hope a 'DNA-fingerprint-reborn' arises from the ashes.
> Alternatively is there someone sensible out there who realises the worth
> of this couple, and offers them a new prestige partnership?
> Wherever you land Thomas, let us know, and we will join you.
> Thank you for past inspiration. Rex
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 04 Sep 2013 11:27:31 -0700
> From: Marleen Van Horne <>
> Subject: Re: [DNA] A Sad Event for Genetic Genealogy
> To:
> Message-ID: <>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> List Members:
>
> I, too, wish to express my sadness that Thomas and Astrid have left FTDNA.
>
> I am not sure that any of us know the exact circumstances, and
> continuing to speculate may be doing a disservice to all parties involved.
>
> The thread IS NOT terminated, but I request that no more posts be made
> on the subject unless you actually have the facts regarding the
> situation. In other words, you are either one of the parties directly
> involved, or have "interviewed" one of the parties and have the facts of
> the issue.
>
> Marleen Van Horne
> Genealogy-DNA List Manager
> --
> When the people,
> who made the music of your youth,
> begin dying of old age,
> you know that you, too, are old.
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 4 Sep 2013 20:17:14 +0100 (BST)
> From: Anders P?lsen <>
> Subject: [DNA] Gok4 ancient Scandinavian farmer and modern European
> variation
> To: "" <>
> Message-ID:
> <>
> Content-Type: text/plain; charset=iso-8859-1
>
> List
> ?
> The Gok4 individual is as the earlier analysed Ste7 individual in the
> previous posts belonging to the Funnelbeaker culture finding in G?khem,
> Sweden and the first farmers in Fennoscandia. However the autosomal DNA
> coverage is for this ancient individual far better than for Ste7. I managed
> this time to match 294k SNPs vs the 1000 genome autosomal panel that I used
> to impute the missing markers for a standard selection of project
> participants and reference populations using phasing and imputation
> software Beagle. These was further LD pruned down to 76k in Plink to get a
> set of unlinked SNPs. The data was then run in Chromopainter-Finestructure
> pipeline unlinked mode using a world panel and then the European panel was
> extracted from the outpul files giving around 63k remainng SNPs for
> analysis.
> ?
> As the results belows shows Gok4 appears to resemble quite much the
> earlier Ste7 individual. The strongest affiliation is with the Sardinians,
> then to Italians, Iberians, Albanians, Croat and Spanish. We also see an
> increased affiliation with populations in Central and Northern Europe like
> British, Scandinavians and Austrians. The most distant populations appears
> to be Saamis, Mordovians and Finns.
> ?
> This appear to suggest some continuity between the first farmers of
> Fennoscandia and the modern Scandinavians. This was not seen in the earlier
> Ste7 analysis but may be due to the low number of markers (6k SNPs) giving
> high margin of error and possible partly different ancestry in Ste7
> (possible Saami like or La Bra?a like ancestry). This analysis however has
> 63k SNP's used in the analysis comparable to the earlier La Bra?a of
> Northern Spain using 68k.
> ?
> Link:
> ?
>
> http://fennoscandia.blogspot.no/2013/08/gok4-and-modern-european-variation.html
> ?
> Anders
>
> ------------------------------
>
> Message: 5
> Date: Wed, 4 Sep 2013 20:19:33 +0100 (BST)
> From: Anders P?lsen <>
> Subject: [DNA] Ire8 ancient Gotland hunter gatherer and European
> modern variation
> To: "" <>
> Message-ID:
> <>
> Content-Type: text/plain; charset=iso-8859-1
>
> List,
> ?
> The Ire8 individual belonged to a 2800-2000 BC Pitted Ware Culture complex
> found in Ajvide, Gotland, Sweden. Ire8 belonged to mtDNA hg U4. The PWC was
> a hunter gatherer culture.?The Ire8 genome had in common 51k SNPs vs the
> 1000 genome reference individuals. These was as with the earlier analysis
> for Gok4, Ste7 and La Bra?as (se earlier posts)? imputed using BEAGLE with
> the same reference panel as before using both project individuals and
> public reference populations. The populations was further LD pruned in
> PLINK down to 22k SNPs and run through Chromopainter-Finestructure unlinked
> pipeline. The European panal was extracted from a world Chromopainter run
> output files resulting in about 19k SNP's for Finestructure analysis.
> ?
> As the results shows from Finestructure heatmap Ire8 appears to give an
> clear clustering to a commom Saami-Finnish box, and at the group level
> appears to be closest to SA1-SA2, Swe-Sam (equal) and Finns3. However we do
> not see a clear clustering as with the La Bra?a's vs the Saamis in the tree
> structure. It seems from the heatmap coloring like Ire8 appears to have
> more southern? ancestry than both the Saamis and the Finns suggesting
> contact with early farmers.
> ?
>
> http://fennoscandia.blogspot.no/2013/08/ire8-and-modern-european-variation.html
> ?
> Anders
>
> ------------------------------
>
> Message: 6
> Date: Wed, 4 Sep 2013 20:22:35 +0100 (BST)
> From: Anders P?lsen <>
> Subject: [DNA] Ajv70 ancient Gotland hunter gatherer and European
> modern variation
> To: "" <>
> Message-ID:
> <>
> Content-Type: text/plain; charset=iso-8859-1
>
> List,
> ?
> The Ajv70 like Ire8 individual belonged to a 2800-2000 BC Pitted Ware
> Culture complex found in Ajvide, Gotland, Sweden. Ajv70 belonged as Ire8 to
> mtDNA hg U4. The PWC was a hunter gatherer culture.?
> ?
> The Ajv70 genome had in common 421k SNPs vs the 1000 genome reference
> individuals. These was as with the earlier analysis for Ire8, Gok4, Ste7
> and La Bra?as (se earlier posts) imputed using BEAGLE with the same
> reference panel as before using both project individuals and public
> reference populations. The populations was further LD pruned in PLINK down
> to 105k SNPs and run through Chromopainter-Finestructure unlinked pipeline.
> The European panel was extracted from a world Chromopainter run output
> files resulting in about 85k SNP's for Finestructure analysis. The high
> number of SNPs should give good resolution for further analysis.
> ?
> The result for Ajv70 above heatmap appears not to give a clear clustering
> to any modern European populations as Ajv70 doesnt fit into any heatbox
> clusters and branch out very early from the rest of the European tree, in
> other words no more systematic affiliation as we have seen in the analysis
> of the Ire8, Gok4, Ste7 and the La Bra?as. There is however no doubt that
> Ajv70 belongs to the more northern populations in Europe if looking at the
> PCA plots below..
> ?
> As we can see from the main variation in thie first dimension D1
> (horizontal) Ajv70 appears to cluster in the same middle area of the plot
> as many populations from especially northeastern continental Europe and
> some of the Scandinavians. The secondary dimension D2 (vertical) appears
> more difficult to explain. Ajv70 and one of the Saami SA2 appear alone on
> the upper part of the plot.but when moving further down the plot looking at
> the upper part of the major cluster not only other Saamis shows up but also
> some of the Vologda Russians, Mordovians, Belorussians, Bulgarians and
> Sardinians..The reason for this could be that there are individuals in
> continental Europe that to larger extent have Ajv70 like ancestry in this
> dimension than many other individuals of their own population.
> Scandinavians and Brits appears to show the most distant to Ajv70 in this
> dimension D2.
> ?
> If looking further to dimension D3 (vertical) on the PCA plot above we get
> a more familiar plot also seen in other analysis. Here we can see Ajv70
> appears to locate between the Scandinavians in the middle of the plot and
> Vologda Russians, Russians and Mordovians.
> ?
> Conclusion:?Ajv70 appears not to fit very well any specific modern
> European population but appears for certain northern, but at group level
> (infered from 289k analysis) from the heatmap colours Ajv70 appears to be
> somewhere between SA4, SWE-SAM,? AUS1, NO6 and EST.
> ?
> This analysis also oppose the following claim about Ajv70 made by other
> genome bloggers that the Ajv's where closest to modern Poles.
> ?
> Link:
> ?
>
> http://fennoscandia.blogspot.no/2013/08/ajv70-and-modern-european-variation.html
> ?
> Anders
>
> ------------------------------
>
> Message: 7
> Date: Wed, 4 Sep 2013 20:24:25 +0100 (BST)
> From: Anders P?lsen <>
> Subject: [DNA] Ajv52 ancient Gotland hunter gatherer and European
> modern variation
> To: "" <>
> Message-ID:
> <>
> Content-Type: text/plain; charset=iso-8859-1
>
> List,
> ?
> The Ajv52 like Ajv70 and Ire8 individual belonged to a 2800-2000 BC Pitted
> Ware Culture complex found in Ajvide, Gotland, Sweden. Ajv70 belonged as
> Ire8 to mtDNA hg U4. The PWC was a hunter gatherer culture.
> ?
> The Ajv52 genome had in common 281k SNPs vs the 1000 genome reference
> individuals. These was as with the earlier analysis for Ajv70, Ire8, Gok4,
> Ste7 and La Bra?as (se earlier posts) imputed using BEAGLE with the same
> reference panel as before using both project individuals and public
> reference populations. The populations was further LD pruned in PLINK down
> to 77k SNPs and run through Chromopainter-Finestructure unlinked pipeline.
> The European panel was extracted from a world Chromopainter run output
> files resulting in about 61k SNP's for Finestructure analysis. The high
> number of SNPs should give good resolution for further analysis.
> ?
> The result seems mostly similar for Ajv52 as for Ajv70. In the above
> heatmap appears not to give a clear clustering to any modern European
> populations as Ajv52 doesnt fit into any heatbox clusters and branch out
> very early from the rest of the European tree, in other words no more
> systematic affiliation as we have seen in the analysis of the Ire8, Gok4,
> Ste7 and the La Bra?as. There is however no doubt that Ajv52 belongs to the
> more northern populations in Europe if looking at the PCA plots below.
> ?
> In the heatmap it seems like CR1, NO6 and NO7 appears to affliate
> strongest on the heatmap, this can however be the effect of these groups
> beeing of only one individual, but if looking at more systematic
> affiliation with larger samples one sees.some weaker affliation to northern
> and northeastern continental European populations and to south-west
> populations. So it might appear like Ajv52 may have some more southern
> ancestry than Ajv70 even they appear similar.On the PCA D1-D3 it seems
> Ajv52 cluster with Scandinavians but not in D1-D2.
> ?
> Link
> ?
> http://fennoscandia.blogspot.no/2013/08/ajv52-and-european-variation.html
> ?
> Anders
>
> ------------------------------
>
> Message: 8
> Date: Wed, 4 Sep 2013 17:03:11 -0500
> From: Rebekah Adele Canada <>
> Subject: [DNA] Gene by Gene launches Free My Genes Site
> To:
> Message-ID:
> <
> >
> Content-Type: text/plain; charset=UTF-8
>
> Hello,
>
> The Gene by Gene parent company has a new site up.
> http://www.freemygenes.org
> It will likely be of the most interest to those who have people with
> breasts in their family trees.
>
> ---
> Regards,
> Rebekah A. Canada
> Volunteer Administrator, Family Tree DNA
>
>
> ------------------------------
>
> Message: 9
> Date: Wed, 4 Sep 2013 12:52:58 -0700
> From: "John O'Grady" <>
> Subject: Re: [DNA] Y DNA analysis from PGP data?
> To: "" <>
> Message-ID: <>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Jim,
>
> Greg Magoon analyzes the Y chromosomes from 1000 Genomes and Personal
> Genome results. His web site is:
>
> www.yfull.com
>
> John O'Grady
>
> >
> > Early this year my genome was sequenced as part of the Personal Genome
> > project, http://www.personalgenomes.org/ So now I have an over 200MB cgi
> > file and am wondering how to put it to good use. Are there tools I could
> > use to look for the SNPs below my haplotype R1b1a2a1a1a3a1, R-Z306?
> > Thanks,
> > Jim Smith
>
>
> ------------------------------
>
> Message: 10
> Date: Wed, 4 Sep 2013 23:14:23 +0200
> From: Itai Perez <>
> Subject: Re: [DNA] A Sad Event for Genetic Genealogy
> To:
> Message-ID:
> <CAPM+otSTYQi9eSdh-gS8wQPVkjDtej6XweFQ=SYfx-iuoAv0=
> g@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Posted by FTDNA on their Facebook page:
>
> "Some have expressed concern about Family Tree DNA staffing. Notably,
> people have heard that Thomas and Astrid Krahn are no longer employed at
> Family Tree DNA. Family Tree DNA has high regard for Thomas and Astrid, for
> their contributions to our company, and the genetic genealogy community.
> Management had a good conversation with Thomas before he left for his
> vacation, and all agreed that upon his return, they would discuss the
> possibility of an alternate working relationship. Out of our respect for
> them, more than that needs to wait for a joint statement we would like to
> make with the Krahns.
>
> Nothing changes in day-to-day operations. Family Tree DNA is dedicated to
> our customers, and none of the routine lab tests have been in any way
> impacted by staffing changes. Where there are lab delays, they are due to
> unfortunate but ordinary lab processes. We are and will remain the company
> of choice for genealogists. Our Genomic Research Center in Houston, Texas
> will continue with everything that it has been doing and more."
>
>
> On Wed, Sep 4, 2013 at 8:27 PM, Marleen Van Horne <> wrote:
>
> > List Members:
> >
> > I, too, wish to express my sadness that Thomas and Astrid have left
> FTDNA.
> >
> > I am not sure that any of us know the exact circumstances, and
> > continuing to speculate may be doing a disservice to all parties
> involved.
> >
> > The thread IS NOT terminated, but I request that no more posts be made
> > on the subject unless you actually have the facts regarding the
> > situation. In other words, you are either one of the parties directly
> > involved, or have "interviewed" one of the parties and have the facts of
> > the issue.
> >
> > Marleen Van Horne
> > Genealogy-DNA List Manager
> > --
> > When the people,
> > who made the music of your youth,
> > begin dying of old age,
> > you know that you, too, are old.
> >
> > -------------------------------
> > To unsubscribe from the list, please send an email to
> > with the word 'unsubscribe' without
> > the quotes in the subject and the body of the message
> >
>
>
> ------------------------------
>
> To contact the GENEALOGY-DNA list administrator, send an email to
> .
>
> To post a message to the GENEALOGY-DNA mailing list, send an email to
> .
>
> __________________________________________________________
> To unsubscribe from the list, please send an email to
>
> with the word "unsubscribe" without the quotes in the subject and the body
> of the
> email with no additional text.
>
>
> End of GENEALOGY-DNA Digest, Vol 8, Issue 703
> *********************************************
>


This thread: