Getting BED file
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6 days ago
maajid • 0

Hii all ,

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

vcf tools annotation • 193 views
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6 days ago
amy__ ▴ 30

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.

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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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