Question

Filtering out by gene and samples from VCF files

1

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4.5 years ago

gprashant17 ▴ 110

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 • 2.0k views

ADD COMMENT • link updated 4.5 years ago by Pierre Lindenbaum 161k • written 4.5 years ago by gprashant17 ▴ 110

score 1 · Answer 1 · 2019-11-04

1

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4.5 years ago

Pierre Lindenbaum 161k

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 '

ADD COMMENT • link 4.5 years ago by Pierre Lindenbaum 161k

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

ADD REPLY • link 4.5 years ago by gprashant17 ▴ 110