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(10-14-2023, 03:12 PM)AimSmall Wrote: (10-11-2023, 09:17 PM)schnurkeramik Wrote: I'm still aligning these
https://docs.google.com/spreadsheets/d/1...sp=sharing
Still aligning?
Are you using pileupCaller by chance?
They're still plugged in, aligning at work, and I'll be back there in a few hours to see if it's done. I have this bash script that calls an mpileup command for all the BAMs there in the folder, so every once in a while I open another shell and run that. Then I use the Java program I wrote to transpose the mpileup output onto the FTDNA haplotree
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Formerly Sheepslayer. Originally Responsible For Identifying Afanasievo Sites As Candidates For Z39589+ Burials
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10-15-2023, 10:01 AM
(This post was last modified: 10-15-2023, 10:10 AM by Jerome.)
(10-14-2023, 09:34 PM)schnurkeramik Wrote: (10-14-2023, 03:12 PM)AimSmall Wrote: (10-11-2023, 09:17 PM)schnurkeramik Wrote: I'm still aligning these
https://docs.google.com/spreadsheets/d/1...sp=sharing
Still aligning?
Are you using pileupCaller by chance?
They're still plugged in, aligning at work, and I'll be back there in a few hours to see if it's done. I have this bash script that calls an mpileup command for all the BAMs there in the folder, so every once in a while I open another shell and run that. Then I use the Java program I wrote to transpose the mpileup output onto the FTDNA haplotree
Can we use Mpileup caller on eigenStrat files for Phenotype/Genotype calls?(HERC2, SLC45A2,Lactose tolerance alleles)
I know it's usually done on BAM files but they are too big for my setup,and eigenStrat files are just shorter and more handy.
Besides I want to do these calls on some older samples from reichLabs website.
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Y-DNA (P): I2-BY79593
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10-16-2023, 04:35 PM
(This post was last modified: 10-16-2023, 04:36 PM by Pribislav.)
It seems most of the remaining BAMs were added to ENA (315/317).
NEO281; 7944-7602 BC; Kotias Klde, Georgia; Mesolithic; J2b2-Z2486* (xZ534) i.e. pre-Z534
Z534 level: Z2486/CTS2582+ A>C (2C); Y2736+ G>T (1T); PF7313+ G>T (1T); Z523+ A>G (2G); Z572+ A>G (1G); Z542+ A>G (1G); PF7297/Z529- G>A (1G); Z534- G>A (5G); Z574- A>G (3A)
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(10-16-2023, 04:35 PM)Pribislav Wrote: It seems most of the remaining BAMs were added to ENA (315/317).
NEO281; 7944-7602 BC; Kotias Klde, Georgia; Mesolithic; J2b2-Z2486* (xZ534) i.e. pre-Z534
Z534 level: Z2486/CTS2582+ A>C (2C); Y2736+ G>T (1T); PF7313+ G>T (1T); Z523+ A>G (2G); Z572+ A>G (1G); Z542+ A>G (1G); PF7297/Z529- G>A (1G); Z534- G>A (5G); Z574- A>G (3A)
Was NEO538 one of those, if you happen to know?
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10-16-2023, 06:45 PM
(This post was last modified: 10-16-2023, 06:52 PM by VladMC.)
(10-16-2023, 06:30 PM)Queequeg Wrote: (10-16-2023, 04:35 PM)Pribislav Wrote: It seems most of the remaining BAMs were added to ENA (315/317).
Was NEO538 one of those, if you happen to know?
Yes.
Pribislav, is it possible to determine the Y-DNA of the sample NEO538?
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(10-16-2023, 06:45 PM)VladMC Wrote: (10-16-2023, 06:30 PM)Queequeg Wrote: (10-16-2023, 04:35 PM)Pribislav Wrote: It seems most of the remaining BAMs were added to ENA (315/317).
Was NEO538 one of those, if you happen to know?
Yes.
Pribislav, is it possible to determine the Y-DNA of the sample NEO538? Brilliant, thank you!
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(10-16-2023, 06:45 PM)VladMC Wrote: (10-16-2023, 06:30 PM)Queequeg Wrote: (10-16-2023, 04:35 PM)Pribislav Wrote: It seems most of the remaining BAMs were added to ENA (315/317).
Was NEO538 one of those, if you happen to know?
Yes.
Pribislav, is it possible to determine the Y-DNA of the sample NEO538?
NEO538; 397-203 BC; Minino, Russia; Iron Age; N1a1a1a1a2-L1026>Z1936>CTS1223>Z1934>Z1928>SK1485 (xFT269439,Y81323,YP6094)
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Does anyone have genotype data for the whole set yet?
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I'll align the new ones in time to analyze them by the time I'm finished looking at the ones I have
Formerly Sheepslayer. Originally Responsible For Identifying Afanasievo Sites As Candidates For Z39589+ Burials
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I see NEO93 and NEO261 are now available. Are they derived for anything downstream of I1? Thanks!
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Y-DNA (P): R-U106-Z18
Y-DNA (M): R-L21-DF13
mtDNA (M): T2f4
mtDNA (P): H1bb
Hoping to see NEO752 and NEO946 available soon.
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Y-DNA (P): E-V257(×M81)
Y-DNA (M): V
mtDNA (P): L2b
NEO145 Hungary Csongrád Gorzsa Cukormajor -4799 Tisza MN E-M132
NEO147 Hungary Csongrád Gorzsa Cukormajor -4774 Tisza MN E-M132
I think this samples E-M35 < V68 < M78 <Z1919< L618
Target: CapsianWGS_scaled
Distance: 1.2510% / 0.01251049
37.2 Iberomaurusian
36.8 Early_European_Farmer
12.8 Early_Levantine_Farmer
8.0 Steppe_Pastoralist
4.8 SSA
0.4 Iran_Neolithic
FTDNA : 91% North Africa +<2% Bedouin + <2 Southern-Levantinfo + <1 Sephardic Jewish + 3% Malta + 3% Iberian Peninsula
23andME : 100% North Africa
WGS ( Y-DNA and mtDNA)
Y-DNA: E-A30032< A30480 ~1610 CE
mtDNA: V25b 800CE ? ( age mtDNA not accurate )
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Target: Russia_EIA_ Late_Kargopol_culture:NEO538
Distance: 3.0546% / 0.03054642
42.4 RUS_Krasnoyarsk_BA:kra001
25.0 RUS_Fatyanovo_BA:I20784
19.6 Russia_EBA_Sakhtish_IIa_Volosovo:NEO187
7.6 Baltic_EST_BA  19_X15_2
4.8 Russia_En_Sakjtish_IIa_Volosovo:NEO188
0.6 RUS_Sintashta_MLBA:I0942
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