Intersect vcf file and bed file

Question

[darklings]

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?

[dariober]

there is no header in the vcf file this may well be the reason why bedtools doesn't recognise your vcf as such. Try adding a header to your vcf file.

[darklings]

I added a header but the same error raised

Answer 1

[Alex Reynolds]

$ bedops --element-of 1 enhancers.bed <(vcf2bed < snps.vcf) > answer.bed

[darklings]

I tried this command but it only created an empty bed file...

[Alex Reynolds]

Maybe your input is unsorted. Try:

$ bedops -e 1 <(sort-bed enhancers.bed) <(vcf2bed < snps.vcf) > answer.bed

You could also run:

$ vcf2bed < snps.vcf | head

to check that conversion from VCF to BED is working.

Failing that, we'd probably need to see what your files actually look like.