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