How many individuals per SNP?

Question

[ritafonsa]

Hi all,

I analysed ddRAD-seq data in Stacks and have a final VCF file.

I want to know how many individuals have each SNP present in my VCF file, so I can plot the distribution of SNPs. I find it easy to know how many SNPs each individual has but not the otherwise.

Any idea?

Thanks in advance,

RIta

Answer 1

[Prash]

Hi Rita VCFtools has an option to find individual IDs, as defined in the VCF header and then you can filter with (-remove option etc)

The other thing would be from many SNPs each individual has, find from a multivenn or use simple bash liners like "diff" to find the individuals with the SNPs

Hope this helps Prash