I have a set of genes and samples from GTEx dataset. I want to filter out variants from a very large VCF file corresponding to these genes and samples. Is there any way to implement the same using VCFtools?
build a bed of your genes , create a complement with 'bedtools complement' and then filter with 'bcftools view --regions-file not-gene.bed the.vcf '
Thanks, filtering out based on the samples (individuals) can be done in the same manner?
Login before adding your answer.
Use of this site constitutes acceptance of our User Agreement and Privacy