Bedtools intersect behavior under different coordinate systems?

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6.3 years ago

edsouza ▴ 30

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.

gene genome • 1.3k views

ADD COMMENT • link 6.3 years ago by edsouza ▴ 30

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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 REPLY • link 6.3 years ago by Kevin Blighe 88k

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