Is it possible to run bayescan with a splitted chromosome?
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2.6 years ago
mataman_lib ▴ 10

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 • 764 views
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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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Two years later I am facing the same issue. I am trying to run bayescan2 (in a smaller set of SNPs than yours) but it is taking forever, 3 days only for the pilot run, not even started the actual calculation. I tried to download the 'new' version of bayescan2 v.2.1 (which they say it can parallelize) but the binary file I download from the website when executed says 2.0... Any alternatives to bayescan to identify loci under selection? Thanks!

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