Question: Filtering out by gene and samples from VCF files
0
gravatar for gprashant17
10 weeks ago by
gprashant1770
gprashant1770 wrote:

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

gtex vcftools snp gene vcf • 114 views
ADD COMMENTlink modified 10 weeks ago by Pierre Lindenbaum125k • written 10 weeks ago by gprashant1770
1
gravatar for Pierre Lindenbaum
10 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum125k wrote:

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 COMMENTlink written 10 weeks ago by Pierre Lindenbaum125k

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

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by gprashant1770
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