Entering edit mode
29 days ago
shu8
•
0
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.
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?
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.
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'
whereleast_depth
is the lowest allowable depth.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.
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.