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 > int.txt
Error: Invalid record in file b.bed. Record is scaffold1090size18908_225 18674 18522
This scaffold looks good to me and in the same format as the other scaffolds. what could be the problem? and please offer suggestions. Thanks