I created a bed file consisting of only exonic coordinates using GTFExtract (GTFUtils) which is a gtf information extraction tool and does not follow the 0 based coordinate system. So my bed file coordinates are same as the gtf file.
I then used bedtools intersect (bedtools v2.25.0) to find if there is any variants present in the exons. Now in the introduction part of bedtools, its mentioned that bedtools takes care of the coordinate system between VCF and BED. Should I be concerned about my resulting results. I did a small experiment with one gene of interest and both cases (one with correct bed format and another with incorrect one) gave out same results.
Hi,
I created a bed file consisting of only exonic coordinates using GTFExtract (GTFUtils) which is a gtf information extraction tool and does not follow the 0 based coordinate system. So my bed file coordinates are same as the gtf file.
I then used bedtools intersect (bedtools v2.25.0) to find if there is any variants present in the exons. Now in the introduction part of bedtools, its mentioned that bedtools takes care of the coordinate system between VCF and BED. Should I be concerned about my resulting results. I did a small experiment with one gene of interest and both cases (one with correct bed format and another with incorrect one) gave out same results.