There are loads of papers recently released and I am way behind. Last two months have me doing deep dive into coding and running apps, don't have time to read "Eurocentric papers" Here is what I got so far. Doing my deep dive I realized Euros have a strangle- hold on these Bioinformatics software but the relief is that not all of them are on the same page. Example. Came across some Russian and French websites that have their own software.
Ok. Here is what I got so far. I am interpreting this to mean the Abusir - JK2888 is East African most closely related to LWK(Kenyan of the Great Lakes) out of YRI, MKK, TSI and CEU.
The Admixture software is IAdmix,
IADMIX
bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0418-7 github.com/vibansal/ancestry spsmart.cesga.es/search2.php Jk2888bam - AbuSIR
Code - using admixture type software
Charts to come
RESULTS
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$ python script
making input file for getting genotype likelihoods
calculating genotype likelihoods for bam file bam_complete_sorted.bam poolsize is: 2
extracting reads covering SNPs from bamfile bam_complete_sorted.bam minQV 13 minMQ 30 maxIS 1000
read 249075 variants from file bam_complete_sorted.bam.ancestry.forGLL
read 249075 variants from file bam_complete_sorted.bam.ancestry.forGLL chromosomes 22
reading sorted bamfile bam_complete_sorted.bam
did not find match for chrom: chr1 in hashtable
did not find match for chrom: chr2 in hashtable
did not find match for chrom: chr3 in hashtable
did not find match for chrom: chr4 in hashtable
did not find match for chrom: chr5 in hashtable
did not find match for chrom: chr6 in hashtable
did not find match for chrom: chr7 in hashtable
did not find match for chrom: chr8 in hashtable
did not find match for chrom: chr9 in hashtable
did not find match for chrom: chr10 in hashtable
did not find match for chrom: chr11 in hashtable
did not find match for chrom: chr12 in hashtable
did not find match for chrom: chr13 in hashtable
did not find match for chrom: chr14 in hashtable
did not find match for chrom: chr15 in hashtable
did not find match for chrom: chr16 in hashtable
did not find match for chrom: chr17 in hashtable
did not find match for chrom: chr18 in hashtable
did not find match for chrom: chr19 in hashtable
did not find match for chrom: chr20 in hashtable
did not find match for chrom: chr21 in hashtable
did not find match for chrom: chr22 in hashtable
did not find match for chrom: chrX in hashtable
did not find match for chrom: chrY in hashtable
did not find match for chrom: chrMT in hashtable
making input file for ancestry calculations
ancestry admixture calculations for bam_complete_sorted.bam poolsize is 2
difficult to estimate admixture coefficients with high confidence
final maxval 0.000000
ADMIX_PROP YRI:0.079985 CHB:0.167553 CHD:0.196781 TSI:0.080717 MKK:0.017754 LWK:0.224568 CEU:0.165074 JPT:0.067569
YRI:0.0800:0.00 CHB:0.1676:0.00 CHD:0.1968:0.00 TSI:0.0807:0.00 MKK:0.0178:0.00 LWK:0.2246:0.00 CEU:0.1651:0.00 JPT:0.0676:0.00 FINAL_ALL_PROPS
YRI:0.0800:0.00 CHB:0.1676:0.00 CHD:0.1968:0.00 TSI:0.0807:0.00 MKK:0.0178:0.00 LWK:0.2246:0.00 CEU:0.1651:0.00 JPT:0.0676:0.00 FINAL_NZ_PROPS bins 200 ssq 0.000000
LL 0.000000 LL_exp 0.000000 0.000000 -nanreal 0m0.296s
user 0m0.000s
sys 0m0.030s
-------------------------------------------------------------------
$ python runancestry.py --freq hapmap3.8populations.hg18 --bam bam_complete_sorted.bam --out bam_complete_sorted.bam.ancestry
$ ancestry --freq hapmap3.8populations.hg18 --bam bam_complete_sorted.bam --out bam_complete_sorted.bam.ancestry
$ python runancestry.py --freq hapmap3.8populations.hg18 --bam chr2.bam --out chr2.ancestry
making input file for getting genotype likelihoods
calculating genotype likelihoods for bam file chr2.bam poolsize is: 2
extracting reads covering SNPs from bamfile chr2.bam minQV 13 minMQ 30 maxIS 1000
read 249075 variants from file chr2.ancestry.forGLL
read 249075 variants from file chr2.ancestry.forGLL chromosomes 22
reading sorted bamfile chr2.bam
did not find match for chrom: chr2 in hashtable
making input file for ancestry calculations
ancestry admixture calculations for chr2.bam poolsize is 2
difficult to estimate admixture coefficients with high confidence
final maxval 0.000000 ADMIX_PROP YRI:0.129015 CHB:0.087100 CHD:0.102989 TSI:0.121688 MKK:0.153969 LWK:0.078015 CEU:0.129280 JPT:0.197942
YRI:0.1290:0.00 CHB:0.0871:0.00 CHD:0.1030:0.00 TSI:0.1217:0.00 MKK:0.1540:0.00 LWK:0.0780:0.00 CEU:0.1293:0.00 JPT:0.1979:0.00 FINAL_ALL_PROPS
YRI:0.1290:0.00 CHB:0.0871:0.00 CHD:0.1030:0.00 TSI:0.1217:0.00 MKK:0.1540:0.00 LWK:0.0780:0.00 CEU:0.1293:0.00 JPT:0.1979:0.00 FINAL_NZ_PROPS bins 200 ssq 0.000000
LL 0.000000 LL_exp 0.000000 0.000000 -nan
real 0m0.296s
user 0m0.015s
sys 0m0.031s
python runancestry.py --freq hapmap3.8populations.hg18 --bam chr2.bam --out chr2.ancestry
IADMIX
bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0418-7 github.com/vibansal/ancestry spsmart.cesga.es/search2.php ./admixture --cv -j2 MinMycNew.bed K
./admixture --cv -j2 input.bed 3
indo-european.eu/human-ancestry/admixture-ancestry-components-r-statistics-plink-convertf-bed-and-ped-files/ adnguyen.github.io/2017_Ecological_Genomics/Tutorial/2017-03-22_Tutorials_PopulGenomics4.html myersgroup.github.io/software.html