Question: Deblock a VCF
gravatar for win
4.3 years ago by
win810 wrote:

Hi all,

I am trying to deblock a gVCF file and it requires an input BED file. While I have the BED files for the standard genomes such as HG18/HG19 etc my question is how do I generate a BED file from the 1000 genomes reference fasta file or say from a custom reference fasta file?

Thanks in advance.

vcf • 1.1k views
ADD COMMENTlink modified 4.1 years ago by Nicola Casiraghi450 • written 4.3 years ago by win810
gravatar for Nicola Casiraghi
4.1 years ago by
Germany, Heidelberg, DKFZ EMBL
Nicola Casiraghi450 wrote:

Hi, getting the lenght of each chromosome of your reference genome (or fasta file), you can use bedtools makewindows to divide it in regions and represent them in bed format.

For example, to divide the human genome into windows of 1MB:

$ bedtools makewindows -g hg19.txt -w 1000000 > hg19_1Mb.bed

where hg19.txt, the file containing chromosome lengths, has the following tab delimited format:

chr1    249250621
chr2    243199373


ADD COMMENTlink written 4.1 years ago by Nicola Casiraghi450
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