tiistai 14. maaliskuuta 2017

Haplotype sharing analysis, part two: Asian connections in Europe

Chromopainter is a software grouping phased data into so called chunks.  Created chunks are a practical implementation of haplotypes.  Usually Chromopainter is used with Finestructure or Globetrotter.  Finestructure reads an input coancestry matrix of individuals created by Chromopainter, which is not the best way to analyze shared chunks between populations, because it doesn't allow you to assign a coancestry connection between populations.  At least I didn't find to way to do it.  Chromopainter does it perfectly and it gives an option to use other softwares in analyzing results.  You can assign donors and recipients at population level.  This of course doesn't mean that the chunk flow goes from donor to recipient, because it is only my definition, but it defines perfectly what is common between population pairs. It neither tells us admixtures, for example the sharing between population x and Saamis tells only how much they share common chunks, not for example how much of  shared chunks are common with putative Siberians, if those Siberians even exist today.

Unfortunately my data is rather limited, some populations are well represented, some other are built only of a few samples.  In future I probably will do more similar tests and try to improve the data.  Just now I consider this step as a showcase of a new method.


edit 14.3.17 17:30

It looks like this works and it is time to play with real data.  Following small test shows how German, Icelandic and Polish haplotype references sort clearly out German and Balto-Slavic speakers, implying higher resolution than genotype data.  

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