bed to vcf format conversion
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
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prathikkv_1992 •
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prathikkv_1992 •
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Input the BED file into the Variant Effect Predictor, and get the output as VCF.
use plink version 1.9 or above and run the following command: plink --bfile my_file_prefix --recode vcf --out my_output_file_prefix
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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