How extract specific SNP position from the bed file-Bedtools

Question

[LionisOne]

I have one bed file with start and end coordinate (range in bed format). I need to extract a specific position from this range bed (for example I need to extract "chr12 25392999" position from the below bed file). How can I do that? could you anyone please help? Appreciate your help! Thanks in advance!

my example bed file looks like this ------>

chr12   25392977    25393116    KRAS_Intron2_Amp7

Answer 1

[Pierre Lindenbaum]

awk -F '\t' '($1=="chr12" && int($2)<= 25392999 && 25392999 <= int($3))'

adjust < , and <= according to : Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems

or

index your bed with tabix and

tabix your.bed.gz "chr12:25392999-25392999"

or

convert your query to bed and

bedtools intersect -wa -u -a database.bed -b query.bed

[LionisOne]

@Pierre Lindenbaum Thanks a lot! Its a great help! I will check and let you know.