Filtering Homeologous SNPs

Question

[swatipuraanik]

Hello,

I read in a recently published article that 'Homeologous SNPs identified from each genotype were eliminated using VCFtools'. Can anyone shed some light on which filtering option in the VCF tools would do that?

Thanks in advance.

Regards
Swati

[Ram]

What are "homeologous" SNPs? Do you mean "homologous", maybe? Please edit your post and add a link to the article you refer to.

[WouterDeCoster]

I guess it's this one: http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0159437

[swatipuraanik]

Yes, the same article, thanks

Answer 1

[harold.smith.tarheel]

The --diff command of VCFtools with --diff-site flag is used to compare VCFs and report unique variants.

Edit: it appears that you want to filter non-homozygous SNPs within a polyploid genome; correct? If so, you can filter by read depth, minimum allele frequency, and minimum quality as described in this publication.

VCF files were first filtered for depth (four reads per genotype covering base of interest) using a custom python script. Then vcftools (Danecek et al. 2011) was run with the following parameters: "–maf 0.35–minQ 30–remove-filtered-all–remove-indels –recode."