aDNA (Dodecad K12b)

[AIexSuvorov]

Admix Results (sorted):

#	Population	Percent
1	North_European	60.47
2	Atlantic_Med	20.46
3	Caucasus	10.23
4	Southwest_Asian	2.29
5	Gedrosia	2.2
6	Siberian	1.87
7	South_Asian	1.22
8	Southeast_Asian	1
9	Northwest_African	0.17
10	Sub_Saharan	0.09

Single Population Sharing:

#	Population (source)	Distance
1	Polish (Dodecad)	4.07
2	Mixed_Slav (Dodecad)	5.99
3	Ukranians (Yunusbayev)	7.29
4	Russian (Dodecad)	8.5
5	Belorussian (Behar)	8.86
6	Russian_B (Behar)	10
7	Mordovians (Yunusbayev)	10.83
8	Russian (HGDP)	10.85
9	Lithuanian (Dodecad)	13.94
10	Hungarians (Behar)	13.96
11	Swedish (Dodecad)	15.55
12	FIN30 (1000Genomes)	16.6
13	Lithuanians (Behar)	17.03
14	German (Dodecad)	17.1
15	Finnish (Dodecad)	18.1
16	Norwegian (Dodecad)	18.89
17	Dutch (Dodecad)	23.88
18	Mixed_Germanic (Dodecad)	24.24
19	Chuvashs (Behar)	24.88
20	CEU30 (1000Genomes)	26.44

 

[Salento]

Torino Lavazza and Bardonecchia

Whole genome sequence data from one individual from Bardonecchia as well as targeted capture sequence data from the 1240K panel from seven individuals from Torino Lavazza and seven individuals from Bardonecchia. All individuals from Torino Lavazza date roughly to the 5th-7th century CE. All individuals from Bardonecchia date roughly to the 6th-8th century CE

ID 936918 - BioProject - NCBI

... with sratoolkit: download sam files and convert to bam (according to the "head" the files are filtered)

bin\sam-dump SRR23560629 | samtools view -b -h - > BARD-T1.bam
samtools index BARD-T1.bam

bin\sam-dump SRR23560650 | samtools view -b -h - > Bard_T2.bam
samtools index Bard_T2.bam

bin\sam-dump SRR23560649 | samtools view -b -h - > Bard_T6.bam
samtools index Bard_T6.bam

... and so on

TEST ... making a dataset:
samtools mpileup -R -B -q 30 -Q 30 -l 1240K_ReichLab.pos -f human_g1k_v37.fasta.gz BARD-T1.bam Bard_T2.bam Bard_T6.bam Bard_T7A.bam Bard_T8.bam Bard_T10.bam Bard_T11.bam Bard_T12.bam To_Lav_T1US6.bam To_Lav_T2US16.bam To_Lav_T10US67_ind1.bam To_Lav_T10US67_ind2.bam To_Lav_T37US60.bam To_Lav_T38US344.bam To_Lav_T90US339.bam | sed 's/chr//' > accumula-questi.txt
./pileupCaller --randomHaploid --sampleNames BARD-T1,Bard_T2,Bard_T6,Bard_T7A,Bard_T8_rid,Bard_T10,Bard_T11,Bard_T12,To_Lav_T1US6,To_Lav_T2US16,To_Lav_T10US67_ind1,To_Lav_T10US67_ind2,To_Lav_T37US60,To_Lav_T38US344,To_Lav_T90US339 --samplePopName LA_Piemonte -f 1240K_ReichLab.snp -e TorBard < accumula-questi.txt

... -e TorBard output Eigenstrat: TorBard.geno TorBard.snp TorBard.ind / -p TorBard output Plink: TorBard.bed TorBard.bim TorBard.fam

... TESTING Dataset:

LA_Piemonte:BARD-T1_1240k,5.50,0.56,2.46,0,34.01,27.30,1.82,0.04,6.48,0.15,19.38,2.29
LA_Piemonte:Bard_T2_1240k,5.98,0.71,2.66,0,42.61,25.66,1.28,0,4.27,0,15.07,1.76
LA_Piemonte:Bard_T6_1240k,6.15,0,2.29,1.16,36.03,25.34,0.22,0.68,7.87,0.29,18.39,1.57
LA_Piemonte:Bard_T7A_1240k,5.81,0,3.36,0.11,32.47,26.05,0,0.24,6.92,0.63,22.22,2.20
LA_Piemonte:Bard_T8_1240k,6.53,0.29,0,2.23,38.66,24.30,0.08,0,4.75,0,20.86,2.30
LA_Piemonte:Bard_T10_1240k,7.94,0,1.82,0.01,38.87,22.27,0,0,8.33,0.02,18.79,1.95
LA_Piemonte:Bard_T11_1240k,8.38,0,2.65,0.27,38.44,24.85,0,0.35,8.35,0.85,13.90,1.95
LA_Piemonte:Bard_T12_1240k,5.83,0,0.42,1.21,36.52,26.01,0.43,0.39,4.08,0.79,22.74,1.59
LA_Piemonte:To_Lav_T1US6_1240k,5.89,0.66,5.51,0,36.12,18.95,0,0,9.82,0,20.96,2.08
LA_Piemonte:To_Lav_T2US16_1240k,6.82,0,1.10,0,36.11,30.75,0.59,0,3.35,2.20,16.94,2.13
LA_Piemonte:To_Lav_T10US67_ind1_1240k,8.12,2.63,0.50,0.11,33.52,36.83,0,0.62,2.35,0.02,12.93,2.38
LA_Piemonte:To_Lav_T10US67_ind2_1240k,7.52,1.55,1.44,0,34.37,32.40,0.66,0,4.92,0.52,13.79,2.83
LA_Piemonte:To_Lav_T37US60_1240k,3.44,0.50,3.86,0,31.30,20.14,0,0,9.12,0,29.42,2.22
LA_Piemonte:To_Lav_T38US344_1240k,5.90,1.32,2.59,0,33.38,17.26,0,1.32,10.75,0,25.62,1.88
LA_Piemonte:To_Lav_T90US339_1240k,8.90,0,1.03,1.80,26.28,22.60,0.18,2.28,10.66,0,25.35,0.92

... WGSExtractv4 coordinates:

BARD-T1,6.06,0.45,2.62,0,32.96,26.80,1.45,0.76,6.13,0.99,18.34,3.45
Bard_T2,6.24,0.93,2.74,0,43.11,24.38,2.10,0,4.46,0,14.08,1.97
Bard_T6,6.53,0,2.33,0.80,38.22,24.79,0.31,0.38,6.75,0.49,18.00,1.39
Bard_T7A,5.21,0,2.29,1.51,32.19,26.35,0.49,0.90,6.30,0.03,22.13,2.60
Bard_T8,7.51,1.00,1.02,2.04,38.58,23.60,0,0,3.97,0,19.65,2.64
Bard_T10,7.08,0,2.19,1.27,37.92,22.53,0,0.56,7.95,0,17.86,2.63
Bard_T11,7.70,0,2.97,0.44,37.33,25.41,0,0.12,7.94,1.54,13.98,2.57
Bard_T12,6.29,0,1.06,1.38,35.41,24.66,0.39,0.60,4.06,0.62,22.90,2.62
To_Lav_T1US6,6.34,1.42,4.60,0,36.21,17.96,0,0,9.65,0,21.76,2.06
To_Lav_T2US16,6.25,0,0,0.25,36.09,30.23,1.05,0,4.21,2.22,17.75,1.95
To_Lav_T37US60,4.39,0.61,3.96,0,31.55,19.82,0,0,8.66,0.14,28.32,2.55
To_Lav_T38US344,5.40,0.07,2.44,1.09,32.93,18.10,0,2.01,10.41,0.47,24.67,2.40
To_Lav_T90US339,9.37,0.65,2.36,1.81,26.31,21.36,0.37,1.16,9.33,0,25.58,1.71
To_Lav_T10US67_ind2,7.51,1.14,0.67,0.31,32.08,32.93,1.52,0,4.60,0.24,15.51,3.47
To_Lav_T10US67_ind1,7.44,2.06,0.56,1.25,32.09,36.33,0,0.96,2.89,0.35,12.81,3.26