Filtering VCF file

Question

[Prakki Rama]

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.

[apl00028]

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

[Prakki Rama]

Hi it is here: https://mbio.asm.org/content/7/2/e02162-15

[apl00028]

I think that each project is different, so I suggest to you asses your data and according with them establish a criteria