Use Stacks with Illumina WGS data

[Beatriz Navarro Domínguez]

Hi everyone,

I've recently obtained some Illumina data from populations of a non-model organism. These data are whole genome sequencing (WGS), with a coverage of 10X, and have not been digested by restriction enzymes.

I wonder if Stacks can be used to analyze this data and build loci for population genomics analysis. Thoughts?

Thanks so much in advance,

Beatriz.

[Catchen, Julian]

Hi Beatriz,

 

This is not possible as Stacks is not designed for shotgun data. However, if you are interested in the population genomics aspects of Stacks, you could call SNPs with another pipeline, export them in a VCF file, then import that VCF file into populations directly, at which point you can use the population maps, filters, exports, etc from populations (for SNP data, not for haplotypes).

 

Best,

 

julian

[Beatriz Navarro Domínguez]

That's great!

Can Stacks handle VCF that are very big? If I have like 100
individuals, and I call snps using a whole genome as reference, the
VCF would be huge.



El mié, 17 may 2023 a las 14:06, Catchen, Julian
(<jcat...@illinois.edu>) escribió:

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[Catchen, Julian]

Well, you would want to only pass the variable sites into Stacks, but otherwise, it can handle pretty big files, depends how much memory your computer has. -julian

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