How to capture the position of SNPs from the gene's locations

1

Hi Guys,

I have a question regarding the annotation of SNPs. I have list of candidate SNPs with chr ids (file 1) and the their positions and another file (file 2) I have a gft file with chr id, gene positions (start and stop) and genes names. I am looking to fetch the positions of SNPs (file 1) in between the positions of genes (file 2). I tried bedtools however I could not file the command. Please advise any options to deal with this analysis.

File 1:
chr1    271353586   T
chr1    897272822   C
chr1    913363908   T

File 2:
chr1    271353222   371353586   Gene1
chr1    897272522   897272822   Gene2
chr1    583821554   583821710   Gene3


Bedtools


Genome


SNPs

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