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liftover.md

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liftover

This tool lifts genomic positions between genome builds. Currently, builds hg19 and hg38 are supported.

Chain files

  • hg19 -> hg38: files/chain/hg19ToHg38.over.chain.gz

  • hg38 -> hg19: files/chain/hg38ToHg19.over.chain.gz

Lift from build hg19 to hg38

This command lifts an input file (regenie.txt.gz) to build hg38 and updates the ID column to chr:pos:REF:ALT.

java -jar /opt/genomic-utils.jar liftover \
--position GENPOS --ref ALLELE0 --alt ALLELE1 --chr CHROM --id ID --update-id \
--chain files/chain/hg19ToHg38.over.chain.gz \
--input regenie.txt.gz --output regenie_hg38.txt.gz