Hi @praveenraj2018

A nice enhancement would be to add an optional argument to filter out RNA editing variants using the REDIportal database.

The process could be run simply as:

1. First convert REDIportal table to bed file

read_tsv("TABLE1_hg38.txt") %>% select(Region, Position) %>% mutate(End = Position+1) %>%
write_tsv(file = "rediportal.bed"), col_names = FALSE)

2. Then run vcftools with --exclude-bed

vcftools --gzvcf sample1.haplotypecaller.filtered.vcf.gz --exclude-bed rediportal.bed --out sample1 --recode --keep-INFO-all

Many thanks,
Oliver