bed to vcf format conversion

Question

[prathikkv_1992]

Hi Guys,new to biostarts and new to bioinformatics. I am trying to convert my output obtained from liftover of hg38 to hg19 which is in .bed format to .vcf format. I am finding no help on google.

.bed ---> .vcf

Thanks in advance

[natasha.sernova]

See these posts:

Create VCF file from .bim, .fam and .bed file

Convert BED(UCSC) to VCF

and this Rpackage description:

http://rpackages.ianhowson.com/cran/bedr/man/bed2vcf.html

Answer 1

[Denise CS]

Input the BED file into the Variant Effect Predictor, and get the output as VCF.

Answer 2

[binodregmi30]

use plink version 1.9 or above and run the following command: plink --bfile my_file_prefix --recode vcf --out my_output_file_prefix