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Post by djoser-xyyman on Mar 16, 2019 19:58:05 GMT -5
The genomic history of the Iberian Peninsula over the past 8000 years Iñigo Olalde1,*, Working on the Iberians olalde2019 using EIGENSOFT convertf -p iberians text file for convertf convertf -p iberians XXXXXXXXXXX/genomes/AncientIberians2019 $ convertf -p iberians.txt parameter file: iberians genotypename: Olalde_et_al_genotypes.geno snpname: Olalde_et_al_genotypes.snp indivname: Olalde_et_al_genotypes.ind outputformat: PACKEDPED genotypeoutname: iberians2019.bed snpoutname: iberians2019.bim indivoutname: iberians2019.fam packed geno read OK numvalidind: 278 maxmiss: 278001 packedped output ##end of convertf run  |
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Post by djoser-xyyman on Mar 16, 2019 20:00:13 GMT -5
Just downloaded the ancient Iberians dataset. Ta! So we have a male with a large proportion of sub-saharan ancestry carrying mtDNA H. |
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Post by djoser-xyyman on Mar 16, 2019 20:02:08 GMT -5
Survival of Late Pleistocene Hunter-Gatherer Ancestry in the Iberia March2019 quote: " Interestingly, CHA002 was assigned to haplogroup R1b-M343, which together with an EN individual from Cova de Els Trocs (R1b1a) confirms the presence of R1b in Western Europe prior to the expansion of steppe pastoralists that established a related male lineage in Bronze Age Europe [3, 6, 9, 13, 19]" So R1b in Europe PRIOR to the supposed Bronze pastoralist yet they continue the delusion. smh Read more: egyptsearchreloaded.proboards.com/thread/2901/peopling-ibiza-neolithics#ixzz5iO1ukEhE |
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Post by djoser-xyyman on Mar 16, 2019 21:25:08 GMT -5
download ancient Iberians from website then convert to PLINK bed
=============
convert EIGENSOFT files to PLINK files
convertf -p iberians.txt
XXXXXXXXXXX/genomes/AncientIberians2019
$ convertf -p iberians
parameter file: iberians
genotypename: Olalde_et_al_genotypes.geno
snpname: Olalde_et_al_genotypes.snp
indivname: Olalde_et_al_genotypes.ind
outputformat: PACKEDPED
genotypeoutname: iberians2019.bed
snpoutname: iberians2019.bim
indivoutname: iberians2019.fam
packed geno read OK
numvalidind: 278 maxmiss: 278001
packedped output
##end of convertf run
=============
clean new PLINK files
plink --bfile iberians2019 --geno 0.999 --make-bed --out iberians2019-fix
==============
convert to VCF
plink --bfile iberians2019-fix --recode vcf --out iberians2019-fix
====================
compress
bgzip iberians2019-fix.vcf
================
tbix index
tabix -p vcf iberians2019-fix.vcf.gz
=============
clean
plink --vcf iberians2019-fix.vcf.gz --const-fid 0 --make-bed --out iberians2019-fix2
=========
admixture at K3
admixture iberians2019-fix2.bed 3
4
5
6
7
8
etc
now to merge with your/my custom dataset
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Post by djoser-xyyman on Mar 19, 2019 14:32:44 GMT -5
Skoglund Ancient Africans
quote:
"Reads were then aligned using the samse algorithm of BWA (version 0.6.1) (Li and Durbin, 2009) using ancient parameters to allow
an increased mismatch rate, and to disable seeding (‘‘-n 0.01 0 2 -l 16500’’). Multiple sequencing runs were run to increase
coverage, and merged together. Duplicates were then removed by identifying clusters of reads which have the same start and
stop position, and the same mapped orientation. The highest base quality representative of each set is used to represent the cluster.
The mix of mitochondrial and nuclear loci necessitates two different references for the alignment process: for mitochondrial analysis,
we use the RSRS (Behar et al., 2012) mitochondrial genome; for nuclear analysis we use the hg19/GRCh37, 1000 Genomes release
reference genome"
The genomic history of the Iberian Peninsula over the past 8000 years
Iñigo Olalde
SI 4 -
Bioinformatics processing
Reads for each sample were extracted from raw sequence data according to sample-
specific indices added during wetlab processing, allowing for one mismatch. Adapters
were trimmed and paired-end sequences were merged into single ended sequences
requiring 15 base pair overlap (allowing one mismatch) using a modified version of
SeqPrep 1.1 (https://github.com/jstjohn/SeqPrep) which selects the highest quality base
in the merged region. Unmerged reads are discarded prior to alignment to both the human
reference genome (hg19) and the RSRS version of the mitochondrial genome (148) using
the ‘samse’ command in bwa v0.6.1 (149).
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Post by djoser-xyyman on Mar 22, 2019 22:23:12 GMT -5
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