How to only keep read that cover a certain region

Question

[nbargues]

Hi, I have aligned ONT data with minimap2 with hg19 as reference.

Now I want to keep only the read that cover entirely a certain region.

I search certain tool like bedtools but didn't find the proper parameter. Any idea how to do that ?

Thanks

[GenoMax]

Check samtools view. Provide a BED file of the region co-ordinates you are interested in.

-L FILE  only include reads overlapping this BED FILE [null]

[nbargues]

It seems to work but I have zero read as output.

I try also this :

bedtools intersect -wa -F 1 -a FAN46998_minimap2_ont.bam -b region.bed > test_intersect.bam

Do you think it's a valid command for my problematic ?