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Thread: Maternal lineages from 10-11th century commoner cemeteries of Hungary

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    Quote Originally Posted by Kaspias View Post
    Well, I did not check how many reads MHper1 had and just picked it randomly to test. It might be about it, too. Anyway, this is an output from .bam extracted by teepan's bam kit. During the process, it also showed me it detects something but resulted in no significant outcome. Wait for yours conclusion, so we can see the situation.
    maybe we could get more SNPs by converting the fastq to BAM? I can send you the fastq converter if you don't have it.

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    Quote Originally Posted by vbnetkhio View Post
    maybe we could get more SNPs by converting the fastq to BAM? I can send you the fastq converter if you don't have it.
    I can try if you send it. I did not have.

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    Quote Originally Posted by Kaspias View Post
    I can try if you send it. I did not have.
    here is what I managed to get.



    only 1% K13 snps are present, it still detects a vague European/Siberian mix.

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    Quote Originally Posted by vbnetkhio View Post
    here is what I managed to get.



    only 1% K13 snps are present, it still detects a vague European/Siberian mix.
    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!

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    Quote Originally Posted by Kaspias View Post
    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!
    this is the sample with the most reads, SHper267. maybe that's why.
    although more reads doesn't necesarily mean more k13 SNPs. maybe some of the samples with less reads have more k13 SNPs.
    Last edited by vbnetkhio; 04-18-2021 at 07:13 PM.

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    Quote Originally Posted by vbnetkhio View Post
    here is what I managed to get.



    only 1% K13 snps are present, it still detects a vague European/Siberian mix.
    Do you know to whom this sample belongs, some conqueror?

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    Quote Originally Posted by Stearsolina View Post
    Do you know to whom this sample belongs, some conqueror?
    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.

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    Quote Originally Posted by Kaspias View Post
    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!
    btw, here is the code I used:

    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
    files used in the code: (snps.txt is a list of ftdna v1 and 23andme v3 snps, because the files are too large otherwise)
    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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