准备文件:
hg19ToHg38.over.chain.gz
hg38ToHg19.over.chain.gz
GRCh37_to_GRCh38.chain.gz
GRCh37_to_GRCh38.chain.gz
下载网页打开很慢,已经放到百度云盘
链接:https://pan.baidu.com/s/1CGQ4TtaibfiMPlkFXSD4yQ
提取码:oqkd
1. bed 文件 hg19转hg38 (GRCH同理)
工具:liftover
liftover只能处理bed格式
liftOver input_hg19.bed hg19ToHg38.over.chain.gz output_hg38.bed unmap.bed
2. vcf文件 GRCH37转GRCH38
工具:vcf-liftover
本质上是调用liftover,速度很快
github链接: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转GRCH38
需要加载参考基因组,速度慢,不是很推荐
##picard 建立参考基因组索引
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 转换坐标
java -jar ~/software/picard.jar LiftoverVcf I= input.vcf.gz 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