1 准备bed文件（R）

rawID <- data.frame(matrix(unlist(rawID),ncol = 3,byrow = T))
colnames(rawID) <- c("chr","start","end")
write.table(rawID,"input.bed",col.names = F,row.names = F,quote = F, sep = "\t")

2 下载坐标转换对应文件，hg38TOhg19

wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz
gunzip hg38ToHg19.over.chain.gz

3 下载转换工具

wget -c http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver
chmod 755 liftOver
./liftOver

4 进行转换

./liftOver input.bed hg38ToHg19.over.chain output_hg19.bed unMapped

5 查看结果

#hg38
cat input.bed | head
chr1    1223243 1223968
chr1    1804418 1806538
chr1    9931890 9934860
chr1    10433841    10442441
chr1    15534236    15536814
chr1    15638306    15643650
chr1    15717892    15721388
chr1    20749722    20773610
chr1    20757165    20773610

#hg19
cat output_hg19.bed | head
chr1    1158623 1159348
chr1    1735857 1737977
chr1    9991948 9994918
chr1    10493898    10502498
chr1    15860731    15863309
chr1    15964801    15970145
chr1    16044387    16047883
chr1    21076215    21100103
chr1    21083658    21100103