WGS variant filtering for exome

Question

[isMM]

Hello everyone, I have a set of WGS data that I have processed until variant calling with freebayes, but I am only interested in conserving the mutations that are found in exonic regions, which would be the most reliable way of accomplishing this?

Thanks in advanced

Answer 1

[Pierre Lindenbaum]

gunzip -c /path/to/your.gtf.gz | awk -F '\t' '($3=="exon") {printf("%s\t%d\t%s\n",$1,int($4)-1,$5);}' | LC_ALL=C sort -T . -t $'\t' -k1,1 -k2,2n | bedtools merge > exons.bed

bcftools view --regions-file exons.bed indexed.vcf.gz