Getting BED file

Question

[Peerzada]

Hi all,

While using vcf.annotation from vcftools, it requires bed file also in input. How can I get that? I have reference genome as well as multisample vcf file for annotation. How do I get the bed file?

Answer 1

[amy__]

If you are using whole exome sequences, then you will find the bed file from the sequencing company/exome panel they used.

If WGS I think you can do bam to bed using bamtobed from bedrolls https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.html

But check this, as that is just my thoughts and I am not an expert.

[Peerzada]

I have a reference from GRCh38 and vcf file of one gene that I obtained .Now I require a bed file for vcf tool annotation.