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How many individuals per SNP?

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

ddrad vcf snps stacks
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updated by Prash • Prash • written by ritafonsa • ritafonsa

1 answer

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

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written by Prash • Prash

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