04-14-2024, 09:56 AM
I hope that there will be volunteers for the little work that I am going to propose.
1) Extract data from Allentoft 2023 (for those who don't have it yet, it's at https://erda.ku.dk/archives/917f1ac64148...chive.html) for the following individuals:
BOO: NEO 60, 61.62
Russia Minino IA: NEO538
Levänluhta IA: DA234,238
Be careful to take the individuals imputed by Allentoft, and not the original data, marked by the suffix “rnd”.
This is all easily done by vcftools ( --keep followed by the list of individual codes as I recalled them). Output a gzipped vcf with "--stdout | gzip >c extract.vcf.gz" )
2) Apply to this gzvcf the program used by McColl et al. 2024 for its research of shared (non-phased) IBDs. This program is IBDseq, available on Browning's page https://faculty.washington.edu/browning/ibdseq.html. It is a small java program that runs quickly and easily. Keep the default settings.
The only slight difficulty with ibdseq is that the program outputs the segments by indicating only their ends. If you want their "length" in centimorgans you have to use an additional program, for example the online service https://hapi-dna.org/query-cm/, but everything is easily done by copying and pasting .
I applied this routine with a bunch of other Allentoft extracts, without encountering anything unusual, except that my results don't really converge much with what McColl says but that's another problem.
So why am I offering this job? Because the results I get for BOO, Minino and Levänluhta are implausible: no shared IBD, not the least. I inspected my vcf without finding anything abnormal, modified (a little blindly) the parameters, nothing works, nothing comes out, everything seems to be working, I don't receive any error message, but the IBDs records are empty (apart from a tiny segment on a single chromosome between two individuals of the same group, I don't remember which one). I can't believe it for a single moment, because qpAdm attests, among other things, to a strong correlation between Minino and Levänluhta.
1) Extract data from Allentoft 2023 (for those who don't have it yet, it's at https://erda.ku.dk/archives/917f1ac64148...chive.html) for the following individuals:
BOO: NEO 60, 61.62
Russia Minino IA: NEO538
Levänluhta IA: DA234,238
Be careful to take the individuals imputed by Allentoft, and not the original data, marked by the suffix “rnd”.
This is all easily done by vcftools ( --keep followed by the list of individual codes as I recalled them). Output a gzipped vcf with "--stdout | gzip >c extract.vcf.gz" )
2) Apply to this gzvcf the program used by McColl et al. 2024 for its research of shared (non-phased) IBDs. This program is IBDseq, available on Browning's page https://faculty.washington.edu/browning/ibdseq.html. It is a small java program that runs quickly and easily. Keep the default settings.
The only slight difficulty with ibdseq is that the program outputs the segments by indicating only their ends. If you want their "length" in centimorgans you have to use an additional program, for example the online service https://hapi-dna.org/query-cm/, but everything is easily done by copying and pasting .
I applied this routine with a bunch of other Allentoft extracts, without encountering anything unusual, except that my results don't really converge much with what McColl says but that's another problem.
So why am I offering this job? Because the results I get for BOO, Minino and Levänluhta are implausible: no shared IBD, not the least. I inspected my vcf without finding anything abnormal, modified (a little blindly) the parameters, nothing works, nothing comes out, everything seems to be working, I don't receive any error message, but the IBDs records are empty (apart from a tiny segment on a single chromosome between two individuals of the same group, I don't remember which one). I can't believe it for a single moment, because qpAdm attests, among other things, to a strong correlation between Minino and Levänluhta.
MyHeritage:
North and West European 55.8%
English 28.5%
Baltic 11.5%
Finnish 4.2%
GENETIC GROUPS Scotland (Aberdeen and Aberdeenshire)
Papertrail (4 generations): Normandy, Orkney, Bergum, Emden, Oulu
North and West European 55.8%
English 28.5%
Baltic 11.5%
Finnish 4.2%
GENETIC GROUPS Scotland (Aberdeen and Aberdeenshire)
Papertrail (4 generations): Normandy, Orkney, Bergum, Emden, Oulu
