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.