bcftools vcf2sex

Question

[williamsbrian5064]

Hi,

I am trying to determine the sex of the samples in a vcf that I have. I use to use the bcftools plugin vcf2sex but I don't see it in the list of plugins when I run bcftools plugin -l. I was wondering if this plugin is no longer available? If this is the case, does anyone have any recommendations of tools to use to get the sex of the samples from a vcf? I saw that were were some R packages that do this but the vcf that I have is huge.

Thanks!

[Raony Guimarães]

Hi, I think so, it's now replaced by guess-ploidy.c

https://github.com/samtools/bcftools/blob/6e58d535b921eaac06984c8fa8b3b23203373e37/plugins/guess-ploidy.c

https://github.com/samtools/bcftools/blob/9aeb1aa92e662da3baed0fe77a7b34bcde9f9b8d/NEWS

Answer 1

[John Marshall]

The NEWS entry for bcftools 1.4 notes that vcf2sex has been replaced by the guess-ploidy plugin.