Hi all,
I currently have a certain list of SNPs (chromosome and position). I need to check whether these SNPs fall into another list of gene regions (chr:start_position-end_position) that I have.
I was previously able to find overlaps between positions using findOverlaps in R and I also saw we can do something similar using bedtools intersect. But it seems like those tools are all for finding chr:start-end overlaps, whereas I want to see whether my SNP positions fall into my gene regions of interest.
Any suggestions would be greatly appreciated.
Thank you!
•
written
by
SGMS
1 answer
$ vcf2bed < snps.vcf > snps.bed
$ gff2bed < genes.gff > genes.bed
$ bedmap --echo --echo-map-id genes.bed snps.bed > answer.bed
The convert2bed binary (vcf2bed and gff2bed) takes care of indexing. You can replace gff2bed with gtf2bed if you have GTF-formatted input.
Log in to answer this question.
-
Intersecting transcriptome bam file with GTF file
written by Jalil Sharif •
-
How to obtain zero-based coordinates read depth using bedtools coverage for a specific region?
written by vladimiralan •
-
Linking SNPs to their summary statistics - if any -
written by SGMS
-
LINK SNPS TO GENES USING BIOMART, KEEPING YOUR INITIAL POSITIONS IN THE RESULTING FILE
written by SGMS
-
Does bedtools intersect output overlaps with isoforms?
written by Kash
-
1000 genomes coding SNPs not in exonic regions?
written by spiral01
-
findOverlaps function in R
written by SGMS
-
Simple gene region plot
written by mitmitrovic •
-
Genomic feature overlaps taking into account underlying sequence feature distributions
written by Sakti
-
How To Intersect A Range With Single Positions
written by roll
not clear. What is the difference ?
With SNPs, I only have a certain position whereas for the region I have chr:start-end. Do you think findOverlaps would work in this case too?
why don't you convert your positions into 1-base intervals ?
I thought so. You mean for example:
1:169549811-169549811
right?
It would be
1:169549810-169549811, because the BED format is 0-based.Thanks. If I want to do that in R though, the positions will remain the same..
Yes, the overlap functions from IRanges/GenomicRanges assume 1-based coordinates.
it seems like there was a discussion about this: A: How To Intersect A Range With Single Positions
Thanks, my search didn't even fall on that one. It seems I will go with Pierre's suggestion and turn the SNP position into a SNP region having basically the same start and end coordinates. And then do the overlap.
Good description of data. It would help if you can post input data and expected output SGMS