Select a single snp in a contig

[Rhewter]

Hi everybody,

I have multiple SNPs per contig in a fasta file. I would like to get just one SNP per contig to reduce the effects of linkage.

How can I do this?


Already, thank you.

[arthurmelo]

Hi Rhewter.. I hope you are well...
The main question before try to help you is understand what SNP do you want to keep. Probably you need to choice some SNP trait like depth or allele frequence and based on some SNP trait decide for one. Do you have potitions for each of them?

[Rhewter]

Hi Rhewter.. I hope you are well...
The main question before try to help you is understand what SNP do you want to keep. Probably you need to choice some SNP trait like depth or allele frequence and based on some SNP trait decide for one. Do you have potitions for each of them?

Hello Arthur,

I am fine and hope you are too.
I just got using R scripts + vcftools. The selection of a single SNP by contig was made using the highest quality grade for the site. I had already filtered through depth and I think for allele frequency is not a good idea because I have only five individuals. But thanks anyway.

One more question ... You've used the snpEff? It has added a new reference to the configuration file?

Hugs from Brazil.

[SNPsaurus]

If you still have the vcf then vcftools allows you to "thin" the SNPs by removing some.

--thin <integer>

Thin sites so that no two sites are within the specified distance from one another.