Is it possible to run bayescan with a splitted chromosome?
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7 months ago

Dear all,

I am analysing whole genome data, which I splitted into 31 chromosomes. My chromosomes in *.vcf.gz format, span from 100Mb to 7.7Gb. Thus, running a Bayescan analysis per chromosome takes an enormous computation time, specially for the largest chromosomes.

Does splitting the chromosomes in smaller pieces alter the final output of bayescan? Do bayescan calculations involve some statistics that need to take all variants into acount? or is each position calculated independently?

Thank you!

bayescan SNP split VCF chromosome • 218 views
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Entering edit mode

Do you have your own answer? I face similar problem. My vcf is include 1.3 millions variants. It is so many variants that bayescan is frozen everytime I run it.

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