Multiple samples/vcf files

[FriederikeHanssen]

IS it possible to plot multiple samples either all in one vcf file or load multiple vcf files at once?

[cccnrc]

Hi @FriederikeHanssen, thanks for reaching out! plotVCF is designed to handle and plot multiple sample in the same VCF file. As example, you can sub-select which samples you want to plot with SAMPLE, differentiate each sample variants with SHAPE, group samples with COLOR_SAMPLE, and much more!

It is not currently possible to load multiple VCF files into plotVCF (if you are interested in helping develop this option we are more than happy to help you out 😉), but you can always merge your different VCF files first (take a look at vcftools merge-vcf or bcftools merge) and then pass the VCF file to plotVCF

I hope it was helpful, do not hesitate to further comment in case you need additional help

[FriederikeHanssen]

Ah great, thank you, missed this earlier. I am not sure my R skills are sufficient to contribute code :D . But merging the vcf files beforehand has worked. My vcf files are quite big (think 80 WGS samples, 50X) , so I am running into memory issues, however this is not very special and I have expected this.

[cccnrc]

You can divide your merged VCF per chromosome (or any other division criteria you like) and run plotVCF on each of them. It is a bit more of work, but it will work as soon as you get to an input VCF size which is compatible with your RAM capacity

[FriederikeHanssen]

yes, true. :) Thanks, for providing this awesome tool. Getting a quick overview is much easier