UCSC FTP path
ftp://hgdownload.soe.ucsc.edu/goldenPath/
1. 通过liftover转换bed文件坐标
1.1 下载转换的chain文件
http://hgdownload.soe.ucsc.edu/downloads.html#human
hg19转hg38 的chain
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz
hg38转hg19 的chain
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz
1.2 下载liftover
可以参考之前的 hunman参考基因组下载及索引建立 中下载的ucsc tools ,使用里面的 liftOver
hg19 bed 转hg38
./liftOver hg19.bed hg19ToHg38.over.chain.gz hg38.bed unmaped.bed
2. 通过 picard 转换 vcf 坐标
2.1 picard 下载,以及建立基因组索引
可以参考之前的 hunman参考基因组下载及索引建立
2.2 vcf坐标转换
java -jar picard.jar LiftoverVcf \
I = input.vcf.gz \
O = output.vcf.gz \
CHAIN = hg19ToHg38.over.chain.gz \
REJECT = unmap_variants.vcf \
R = hg38.fa # ref genome