Biostar Beta. Not for public use.
Filtering VCF file
Entering edit mode
13 months ago
Prakki Rama ♦ 2.3k

Hi all,

I am trying to filter VCF file based on a publication with the following criteria.

Base calls derived from these two Vcf files were then retained only if

(1) the proportion of high-quality bases supporting the call was ⱖ90%,

Is this same as setting DP4/DP >= 90%?

(2) 5 high-quality bases were required as a minimum

So I assume DP4=5 here

(3) the root of the mean square mapping quality of reads covering a putative variable site was ⱖ30;

So, I assume MQ = 30 here

(4) the Phred scaled quality supporting a base call was ⱖ25;

what is the appropriate filter to set for this?

Edit: Is this same as QUAL >= 25?

(5) reads spanning the putative variable site were made up of ⱖ35% high-quality bases.

what is the appropriate filter to set for this?

many thanks for your answers in advance.

Entering edit mode

Could you show us which publication is it? Because each publication show different criterias


Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.1