Samtools depth input

Question

[Fatima]

Hello everyone,

I have a genebank file that I want to convert to bed to use as samtools depth input. I used this script: But start positions are actual start positions minus 1

start = feature.location.start.position stop = feature.location.end.position

for example if a gene starts from 350 to 2000 in gb file, in the bed format it's 349 to 2000, but again samtools depth results start from 350!

Is the converting script correct, or should I use start = feature.location.start.position+1

Thank you for your time.

[ATpoint]

The output is simply 1-based, right?

Answer 1

[GenoMax]

This should prove useful: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems

BED format is zero-based.