Remove genes that each of a gene with multiple SNVs

Question

[zengtony743]

I generated a vcf file with snpEff annotation tool . In this file, there are many genes needed to be removed because a gene with multiple SNVs, these are all false positive SNVs that I need to remove. Is there tools can do this? I usually do manually by transferring vcf to a txt format file and then excel file using annovar package. Is there tools can do this by running a script by not by excel table ?

[venu]

Please respond quickly and remove other(same) questions of your.

[zengtony743]

Thanks ! Just don't know what's going on with my cell phone today

Answer 1

[Alex Reynolds]

Say your threshold is one SNP per gene, and you have a file of SNPs called snps.vcf and a BED file containing gene annotations called genes.bed. You could use vcf2bed and bedmap:

$ vcf2bed < snps.vcf > snps.bed
$ bedmap --count --echo --delim '\t' genes.bed snps.bed \
    | awk '$1==1' \
    | cut -f2- \
    > genes_with_one_overlapping_snp.bed

Or as a one-liner:

$ vcf2bed < snps.vcf | bedmap --count --echo --delim '\t' genes.bed - | awk '$1==1' | cut -f2- > genes_with_one_overlapping_snp.bed

[zengtony743]

Thanks Alex, this is the first time to use vcf2bed,

When i run

$ perl PATH/vcf2bed.pl —keep-header < my_file.vcf

It shows

Cannot open --keep-header at PATH/vcf2bed.pl line 12

my_file.vcf works fine, did I miss something?

[Alex Reynolds]

I'm not sure what vcf2bed.pl is. You might take a look here and see if you have this installed? https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/vcf2bed.html