vcf-compare alternative in R

Question

[User6891]

Hi,

I'm wondering if there is an alternative to vcf-compare in R. I would like to get the number of common/unique variants between two vcf files.

I use the readVcf function of the VariantAnnotation package to read my vcf files in R.

Answer 1

[a.alnawfal.1992]

Hi, i did not use R to Compare 2 vcf files, but i used RTG-tools and Hap.py for validation purpose where GIAB recommend to use one of these tools and both provide you the result as :

1. TP : the variants in both files
2. FP: the variants found in the Quary (Second) file but not in the true file (First)
3. FN: the variants in the True but not in the Quary.

check there website:

https://github.com/RealTimeGenomics/rtg-tools

https://github.com/Illumina/hap.py