Can Plink Be Used For The Analysis Of A Bacterial Dataset?

Question

[alphaace]

Hi,

Is it possible in plink to specify a non-human chromosome in the map file? I am curious if it can be run on a bacterial data set that only has 2 chromosomes and is haploid?

On the site it says:

By default, each line of the MAP file describes a single marker and must contain exactly 4 columns:

 chromosome (1-22, X, Y or 0 if unplaced)
 rs# or snp identifier
 Genetic distance (morgans)
 Base-pair position (bp units)

However, what if I just label everything chromosome 1 or 2?

Thanks!

[zx8754]

It is not a "must" to have all chromosomes, you can run analysis on 1 chromosome if needed. But someone else should comment if Plink can be used for analysis of bacterial data.

[d.s.account]

This is true, one can use --allow-extra-chr. But whatever I try I cannot find a work-around to solve that all my .vcf do not have GT entries.

Answer 1

[Neilfws]

If you read about the types of analysis that PLINK can do at the website, it's pretty clear that it's designed for humans. Or at least, diploid organisms which reproduce sexually, have chromosomes that undergo recombination and have sub-populations defined by SNPs. I'd also question whether bacteria even have SNPs in any meaningful sense.

[Zev.Kronenberg]

Neilfws is right, do NOT go down this route. I have and it was an epic waste of time.

[alphaace]

Thank you everyone for the info. I guess I'll look at something else...Any suggestions?

[Zev.Kronenberg]

What analyses are you trying to accomplish? What data do you have? Could you edit your question to include this information?

[d.s.account]

Do you know anything about what tools are recommended then?

Answer 2

[d.s.account]

You can try my protocol:

What is the best way to perform a PCA on .vcf of closely related bacteria?