VCFfiltering

Question

[Peter]

Hi,

A) I have a large set of samples diploid, tetraploid, and hexaploid mixed. I have used FreeBayes to build a VCF file. I want to filter the VCF file, some of my filters I have already applied in FreeBayes.

freebayes -f ref.fa -m 40 -q 10 -g 100 --min-coverage 5

I want to further filter the VCF for MAC > 3 ; missing data cut off 0.75

FreeBayes has vcffilter. Can I apply these filters there?

B) I want to apply the slightly different filter for analysing the diploids in bcftools

minimum mapping quality >40 ; 
minimum genotype quality score >10 ; 
maximum coverage 100 ; 
minimum coverage read depth 5 ; 
consider only biallelic loci ; 
MAC > 3 
missing data cut off 0.75

How can I run this in bcftools?

Answer 1

[Mark]

Tutorial on how to use bcftools filter: https://samtools.github.io/bcftools/howtos/filtering.html