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Received: 3,471 Given: 1,541 |
Thumbs Up |
Received: 3,471 Given: 1,541 |
Thumbs Up |
Received: 11,836 Given: 7,303 |
How did you manage to reach snp number that admixture studio needs?
I tried to convert fasta to bam and it ended up with literally 0 snps in autosomal data. I tried with another sample, using directly the bam shared, and see such ratio:
-----------------------------------------------------------
12 ancestral populations
166770 total SNPs
1 flipped SNPs
0 heterozygous SNPs
0 no-calls
166764 absent SNPs
0.000036 genotype rate
Fewer than 100 usable SNPs!
Thumbs Up |
Received: 3,471 Given: 1,541 |
Thumbs Up |
Received: 52,721 Given: 43,621 |
Thumbs Up |
Received: 3,471 Given: 1,541 |
SHper267 (Sárrétudvari-Hízóföld/267) from this study. So it's actually a commoner?
mtdna : D4b1
closest mtdna matches in: Kazakhstan, Mongolia
burrial info: sub-adult infantia silver penannular hair ring, string of beads (withs shells), braid ornaments, silver braclet 10.
Sárrétudvari-Hízóföld (Hajdú-Bihar County)
The site was excavated between 1980 and 1985 under the leadership of Ibolya M. Nepper [18].
The site with 262 graves is considered the largest 10th
-century cemetery in Hungary. The
cemetery contains very high proportion of burials with weapon- (archery equipment, sabers,
ax) and horse riding-related (eg: pear-shaped stirrups) grave-goods, and the archeological
findings consist of jewelry - hoops around the head (penannular hair rings), neck jewelry
(neckrings, beads), arm jewelry (e.g., bracelets, beads), - dress fittings, and implements (e.g.,
knives, fire-lightning equipment). Based on the composition of the findings and the lack of
coins and grave-goods dated to the reign of the kings of the Árpád dynasty, the cemetery can
be dated to the 10th century. Formerly it was classified as a commoner cemetery, and in the new
classification it belongs to the 10th
-century village cemeteries.
The skeletal remains are of good / medium preservation. During the extensive anthropological
analysis (e.g., [21]), 265 individuals were determined, of whom 98 belonged to sub-adult- and
162 skeletons to adult categories. Based on the skulls suitable for taxonomic studies, the series
shows European characteristics with the presence of cromagnoid and nordoid elements.
Last edited by vbnetkhio; 04-18-2021 at 06:39 PM.
Thumbs Up |
Received: 3,471 Given: 1,541 |
btw, here is the code I used:
files used in the code: (snps.txt is a list of ftdna v1 and 23andme v3 snps, because the files are too large otherwise)Code:plink2 --vcf bam_chr1.vcf.gz --make-bed --out chr1 --set-missing-var-ids @:# plink2 --vcf bam_chr10.vcf.gz --make-bed --out chr10 --set-missing-var-ids @:# plink2 --vcf bam_chr11.vcf.gz --make-bed --out chr11 --set-missing-var-ids @:# plink2 --vcf bam_chr12.vcf.gz --make-bed --out chr12 --set-missing-var-ids @:# plink2 --vcf bam_chr13.vcf.gz --make-bed --out chr13 --set-missing-var-ids @:# plink2 --vcf bam_chr14.vcf.gz --make-bed --out chr14 --set-missing-var-ids @:# plink2 --vcf bam_chr15.vcf.gz --make-bed --out chr15 --set-missing-var-ids @:# plink2 --vcf bam_chr16.vcf.gz --make-bed --out chr16 --set-missing-var-ids @:# plink2 --vcf bam_chr17.vcf.gz --make-bed --out chr17 --set-missing-var-ids @:# plink2 --vcf bam_chr18.vcf.gz --make-bed --out chr18 --set-missing-var-ids @:# plink2 --vcf bam_chr19.vcf.gz --make-bed --out chr19 --set-missing-var-ids @:# plink2 --vcf bam_chr2.vcf.gz --make-bed --out chr2 --set-missing-var-ids @:# plink2 --vcf bam_chr20.vcf.gz --make-bed --out chr20 --set-missing-var-ids @:# plink2 --vcf bam_chr21.vcf.gz --make-bed --out chr21 --set-missing-var-ids @:# plink2 --vcf bam_chr22.vcf.gz --make-bed --out chr22 --set-missing-var-ids @:# plink2 --bfile chr1 --extract snps.txt --make-bed --out chr1_filtered plink2 --bfile chr10 --extract snps.txt --make-bed --out chr10_filtered plink2 --bfile chr11 --extract snps.txt --make-bed --out chr11_filtered plink2 --bfile chr12 --extract snps.txt --make-bed --out chr12_filtered plink2 --bfile chr13 --extract snps.txt --make-bed --out chr13_filtered plink2 --bfile chr14 --extract snps.txt --make-bed --out chr14_filtered plink2 --bfile chr15 --extract snps.txt --make-bed --out chr15_filtered plink2 --bfile chr16 --extract snps.txt --make-bed --out chr16_filtered plink2 --bfile chr17 --extract snps.txt --make-bed --out chr17_filtered plink2 --bfile chr18 --extract snps.txt --make-bed --out chr18_filtered plink2 --bfile chr19 --extract snps.txt --make-bed --out chr19_filtered plink2 --bfile chr2 --extract snps.txt --make-bed --out chr2_filtered plink2 --bfile chr20 --extract snps.txt --make-bed --out chr20_filtered plink2 --bfile chr21 --extract snps.txt --make-bed --out chr21_filtered plink2 --bfile chr22 --extract snps.txt --make-bed --out chr22_filtered plink --bfile chr1_filtered --merge-list list.txt --make-bed --out SHper267 plink2 --bfile SHper267 --export vcf
https://filebin.net/hpcyzve5pkf77rnr
and then I converted the resulting vcf to 23andme with dnakitstudio.
I used the ft_23 template, it's also there in the filebin.
did you use "--set-missing-var-ids @:#"? otherwise there are no rsids in the output.
Last edited by vbnetkhio; 04-18-2021 at 07:22 PM.
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