How many individuals per SNP?
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2.5 years ago
ritafonsa • 0

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 • 540 views
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Entering edit mode
2.5 years ago
Prash ▴ 280

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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