How can I filter by read depth using vcftools?

Question

I am trying to build a workflow to analyse my scRNA-seq data. I am using a combination of GATK and samtools, vcftools, bcftools. I would like to filter my .vcf file such that it removes all entries that have fewer than 10 reads. It looks like vcftools can be used for this. My code is:

vcftools --vcf "$fn" --out "$fn"_dp10 --minDP 10 --recode --recode-INFO-all

However, it does not filter out anything. Any thoughts on this?

Kind regards Cora

score 2 · Answer 1 · answered Jan 25 '21 at 09:03

2

I just found the answer! I had to use --mean-minDP instead of --minDP.

Kind regards Cora

answered Jan 25 '21 at 09:03

Cora_olpe

43
7

VCFtools (v0.1.17) `Error: Unknown option: --mean-minDP` – Kermit May 27 '23 at 11:12

score 0 · Answer 2 · answered May 27 '23 at 11:31

0

One source of --minDP not working is a parsing bug that emits a warning, but does not error.

https://github.com/vcftools/vcftools/issues/134

answered May 27 '23 at 11:31

Kermit

4,922
4
42
74

How can I filter by read depth using vcftools?

2 Answers2