Question: Bedtools intersect behavior under different coordinate systems?
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gravatar for edsouza
11 months ago by
edsouza30
edsouza30 wrote:

I'm currently waiting for a pipeline I'm running to produce some BED files and VCF files, which I will then intersect with a GFF file of genes that I want. The command I'm running will be:

bedtools intersect -wa -wb -a file.bed -b searchSpace.gff > out.bed
bedtools intersect -wa -wb -a snps.vcf -b searchSpace.gff > out.vcf

I know that GFF runs under a different coordinate system than BED or VCF format. I also know that bedtools natively accepts these types of files. My question is, when I use the -wa -wb option to write the coordinate features from both input files, will there be a discrepancy in the output? Or will bedtools automatically take care of that? I need to know whether it's necessary to take the extra step of converting all of my GFF files to BED coordinate system, or if doing so will result in a double-correction by bedtools.

genome gene • 298 views
ADD COMMENTlink written 11 months ago by edsouza30

Apologies but your question appears strange... Why do you not just execute these commands to see what they produce? Then, you will be enlightened.

ADD REPLYlink modified 11 months ago • written 11 months ago by Kevin Blighe45k

I figured I'd ask in case anybody else had the question and wanted to quickly find an answer by googling it.

ADD REPLYlink written 11 months ago by edsouza30

Okay, and is everything okay now?

ADD REPLYlink written 11 months ago by Kevin Blighe45k
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