Hello All, I am trying to perform intersection between with my bed file and vcf and I keep getting errors.my bed files is a call of all the genes in the ORFs. The following is the command I am using and the errors.
bedtools intersect -a a.vcf -b b.bed -wa
- Please ensure that your file is TAB delimited (e.g., cat -t FILE).
- Also ensure that your file has integer chromosome coordinates in the expected columns (e.g., cols 2 and 3 for BED).
I tried to do cat -t a.vcf to TAB it but still get the errors. I will appreciate your suggestions. Thanks in advance.