VCF filter by read depth

Question

[shu8]

Hi all

I would like to inquire about a question regarding VCF file. The information said that the VCF file is text file, and it can be opened on PC using Notepad. However, when I tried to use Notepad to open it, there are a lot of garbled information. I would like to inquire what cause this. Additionally, the approach of the VCF file is from the storage drive, and I would like to inquire whether it causes this troubleshooting. I greatly appreciate your help.

[Ram]

Hang on, your title says you wish to filter VCF by read depth but your post looks like written by someone who doesn't know VCF files. What's happening here?

[shu8]

I apologize for any inconvenience. I would like to inquire whether it is possible to know the read depth of coverage and the base from the VCF file. I greatly appreciate your help.

[Ram]

It's no inconvenience, I was just clarifying what your goal is here. You can use bcftools view to filter using read-depth. You should use either -i 'INFO/DP > least_depth' or -e 'INFO/DP < =least_depth' where least_depth is the lowest allowable depth.

[Ram]

The information said that the VCF file is text file, and it can be opened on PC using Notepad.

First part is right, second part is a bad idea. Use notepad++ if you have to, but opening a VCF file (especially one that >10MB) on a PC takes a LOT of RAM.

when I tried to use Notepad to open it, there are a lot of garbled information

Are you sure you're trying to open a VCF file and not a vcf.gz file? It's either that or a valid VCF looks garbled to you as someone new to the format. Please read the VCF spec document to know what to expect.