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Extracting variants from genic region

Dear community, I am doing a whole-genome phylogenomic analysis of a diploid fungus. I took only the primary (considering it as a collapsed assembly) contigs of phased assembly as a reference and aligned whole-genome sequencing reads of more than 150 isolates. I did extensive variant filtering but still, the number of the variants across all 150 isolates are too high to be handled. Hence I thought to only take variants from the genic region for further analysis. Therefore I have the following questions

Would this be okay if I only take variants in the genic region for further analysis?

If it is okay to use the genic region for population genetic analysis then could someone suggest to me how I best extract variants from the genic region (with the help of a gff file, I guess) from the multi-samples vcf file which I have generated using freebayes. Thanks

snp
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by nagarsaggi • nagarsaggi

1 answer 

awk -F '\t' '($3=="exon") {printf("%s\t%d\t%s\n",$1,int($4)-1,$5);}' file.gtf |\
     sort -T . -t $'\t' -k1,1 -k2,2n | bedtools merge > exons.bed

bcftools view -O z -o exons.vcf.gz --regions-file exons.bed indexed.vcf.gz
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written by Pierre Lindenbaum Pierre Lindenbaum

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