Filtering out by gene and samples from VCF files
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18 months ago
gprashant17 ▴ 70

Hi,

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?

Thanks

vcf SNP vcftools gtex gene • 687 views
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18 months ago

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 '

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Thanks, filtering out based on the samples (individuals) can be done in the same manner?

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