Having a deletion coordinates how to know in which gene this is?

Question

[Manuel]

I have a VCF files with big deletions and I want to know if these deletion are in (completly or partially) of a particular gene. I want to basically know the gene names affected by these deletions

Answer 1

[kashiff007]

Simply annotate your VCF file using any of the program; ChIPseeker, MEME, bcftools ... the list is long. I am demonstrating bcftools here:

   bcftools annotate  -a genes.bed.gz  -c CHROM,FROM,TO,GENE  -h <(echo '##INFO=ID=GENE,Number=1,Type=String,Description="Gene name">')  variants.vcf.gz

A few things to note:

• genes.bed.gz must be a standard BED file that has been zipped using bgzip (bgzip genes.bed)
  • genes.bed.gz must indexed using tabix (tabix -p bed genes.bed.gz)
  • genes.bed.gz does not need a header (we define this with the -c option instead)
  • CHROM', 'FROM', and 'TO' are required to be passed to the -c option, but these columns do not actually get added to your VCF (only the '- GENE' will get added)
  • Because we're not annotating from a VCF/BCF file, the -h option is required (it will not work otherwise)
  • Whatever we pass to the -h option will simply get added to the VCF meta-information

Answer 2

[lieven.sterck]

what have you tried so far?

quick search should give you half the solution already (bedtools intersect)

[Manuel]

Thanks for the answer.

If I do this, I would need a dataset with genes name and their coordinates wouldn't I?

[lieven.sterck]

yes indeed. a GFF or GTF or such file with the gene annotations or bed-file might be even more suited.

[Manuel]

many thanks for your help

Answer 3

[brunobsouzaa]

Besides everything that was already said, you can also try using AnnotSV for this task.