utility to convert coordinates of variants in VCF files between different genome builds.

Install via pip:

pip install vcfremapper

vcfremapper PATH_TO_VCF CONVERTED --reference genome.fa

# or pass output to bgzip
vcfremapper PATH_TO_VCF --reference genome.fa | bgzip > CONVERTED

# or pipe in gzipped data
cat PATH_TO_VCF | vcfremapper --reference genome.fa | bgzip > CONVERTED

Options:

• --reference - path to reference genome, for the build being converted to.
• --build-in - build to convert from, defaults to hg19
• --build-out - build to convert to, defaults to hg38
• --tempdir - folder to save uncompressed temp file in before sorting