depth2cov is not available

[Golden-proteogenomics]

Helllo,
I'm trying to use our script depth2cov, but I wasn't able to access the link your provided: "depth2cov is a program that converts the output of samtools depth to .cov format. Its source code is available here."

Unfortunately, the like leads to a "404 - Page Not Found" error. Could you kindly provide some guidance or an updated link? I'd really appreciate your help!

Best,
Shuai

[mobinasri]

That program is deprecated instead you can use bam2cov to convert bam to coverage file directly. please follow the instructions here:
https://github.com/mobinasri/flagger?tab=readme-ov-file#1-create-a-whole-genome-bed-file
https://github.com/mobinasri/flagger?tab=readme-ov-file#2-convert-bam-to-cov