'How can I filter my R dataframe based on a column match AND ranging values?

I am trying to filter a VCF file based on chromossome and genomic range that is present in my annotation file.

My annotation file looks like this:

And my VCF file:

CHROM	POS	ID	REF	ALT
chr1	3	.	A	G
chr10	6020671	.	T	C
chr11	36591872	.	T	G
chr11	36567002	.	G	A

So, I need filter my VCF based on CHROM match and variant position ranging between the annotation values "START" and "END".

Is there an easy way?

Solution 1:^[1]

Not on R, but the annotation file is in .bed format and the other file is a vcf so you can use

bedtools --intersect

the command line: bedtools intersect -a <FILEA> -b <FILEB>

To sort the bedfile by chrom and by pos: sort -k1,1 -k2,2n in.bed > in.sorted.bed

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Solution	Source
Solution 1	ekerde