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?
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written
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Peerzada •
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.
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.
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