bed vcf file GRCH37 (hg19) turn GRCH38 (hg38)

 

 

Preparing Files:

hg19ToHg38.over.chain.gz

hg38ToHg19.over.chain.gz

GRCh37_to_GRCh38.chain.gz

GRCh37_to_GRCh38.chain.gz

Download pages open very slowly, it has been put Baidu cloud disk

Link: https: //pan.baidu.com/s/1CGQ4TtaibfiMPlkFXSD4yQ
extraction code: oqkd

1. bed hg19 file transfer hg38 (GRCH Similarly)

Tools: liftover

liftover format can only handle bed

liftOver input_hg19.bed  hg19ToHg38.over.chain.gz output_hg38.bed unmap.bed

2. vcf file GRCH37 turn GRCH38

Tools: vcf-liftover  

Essentially calling liftover, fast

github link: https://github.com/liqg/vcf-liftover

zcat input.vcf.gz | ~/vcf-liftover GRCh37_to_GRCh38.chain.gz | bgzip -c > output.vcf.gz

3.picard GRCH37 turn GRCH38

Need to load the reference genome, slow, not very recommended

## picard establish a reference genome index

java -jar ~/picard.jar CreateSequenceDictionary \

        R= ~/GRCH38/Homo_sapiens.GRCh38.97.dna.primary_assembly.fa O= ~/GRCH38/Homo_sapiens.GRCh38.97.dna.primary_assembly.dict

## picard coordinate conversion 
Java -jar ~ / Software / picard.jar LiftoverVcf input.vcf.gz the I = O = output.vcf.gz \
        CHAIN= ~/GRCh37_to_GRCh38.chain.gz  REJECT=unmap_rejected_variants.vcf R=~/GRCH38/Homo_sapiens.GRCh38.97.dna.primary_assembly.fa