SNP input data for Arlequin

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5.4 years ago

mahnazkiani ▴ 60

I got the population.haps.vcf file from Stacks and converted to .arp file using PGDSpider, but still is not working in Arlequin. I appreciate your help for preparing Arlequin input file. I have 48 samples from 8 populations. Do I need to edit the file?

Thanks!``

ddRAD • 3.1k views

ADD COMMENT • link updated 3.0 years ago by strive • 0 • written 5.4 years ago by mahnazkiani ▴ 60

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What is your issue? I have ran across the issue of Arlequin not showing any progress during an analysis, and just had the analysis done in DnaSP instead.

ADD REPLY • link 5.4 years ago by Gio12 ▴ 220

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I tried to use DnaSP as well but when I convert my data to .NEXUS by PGDSpider it is not readable in DnaSp

ADD REPLY • link 5.4 years ago by mahnazkiani ▴ 60

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Hi:

Have you solved your problem? I have also been using Arlequin recently and have encountered the same problem, but I don't know how to deal with it, do you want to talk about it? (The VCF file is obtained by stacks v2.55)

Thanks

Ling

ADD REPLY • link 3.0 years ago by strive • 0

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