Hi, I want to intersect my vcf files with the enhancer database bed file; so I used bedtools and print:
bedtools intersect -a enhancers.bed -b examples.vcf
then it showed
Error: Type checker found wrong number of fields while tokenizing data line.
Do the bed or vcf files contain too many fields? But I don't want to cut the columns, or maybe I should annotate my vcf file?
The vcf file looks like:
#CHROM POS ID REF ALT QUA FILTER AA ....... (so many columns) (and datas below, actually there is no header in the vcf file)
And the bed file looks like:
chr1 839741 840250 chr1:839741-840250 24 . 839787 839788 0,0,0 2 20,436 0,73
Can anyone help me to solve the problem?
there is no header in the vcf filethis may well be the reason why bedtools doesn't recognise your vcf as such. Try adding a header to your vcf file.
I added a header but the same error raised