Hi Kalpita,

for merging multiple VCF files into one, there are multiple tools (Bcftools-merge, GATK CombinedVariants, Picard MergeVCF, and so on)

I recommend using bcftools. The following link might be helpful:

https://www.biostars.org/p/311621/

For converting this to .csv or .xls, once you get your final vcf file with all the individuals, you can open it in R and save in different formats.

I hope this is of some help.

Thanks.

thank you Abhinav Tyagi . I have a single vcf file with multiple variants either on teh same chr or different chr /sample. If I were to know freq of variants across each chr, would there be an R package or tool you would know of?

Also, is there a quick tool to visualize variants apart from IGV which in not very complex on any platform of R or Python?

Hi Kalpita,

to know the allele frequency at each variant site you can use vcftools (--freq option). To the freq of variants per chromosome, I can think of writing a simple R script which can do. Just convert your vcf file into csv and retain only the first 3 characters (which will be the genotypes) per column. You can use that to calculate whatever you wish to.

Thanks Abhinav Tyagi ! Will try to write some code. I see that Galaxy also has some interesting tools to handle and visualize output files.

You may try this commandline tools https://github.com/everestial/VCF-Simplify

It is very minimalist and has a thorough tutorial to activate different flags; so you get the data you want.

thank you Bishwa Giri ! Seeing this after a while. Will see if it is useful. My vcf files are from a custom script and don't generate index files, hence I face issue running many tools that need indexing.