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