参考:不同参考基因组版本间 bed vcf文件转换_风风是超人的博客-CSDN博客
下载hg19的2bit文件
wget https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit
下载2bit to fasta工具,将2bit格式的参考基因组转换为fasta格式
$ rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/ ./
$ ./twoBitToFa hg19.2bit hg19.fa
建立samtools索引:samtools的安装和使用 - 简书
建立BWA索引:BWA使用详解 - 知乎
下载picard工具包,对hg19.fa建立索引
下载hg38转hg19 的chain
$ ./samtools faidx hg38.fa
$ bwa index -a bwtsw hg38.fa
$ wget https://github.com/broadinstitute/picard/releases/download/2.23.0/picard.jar
$ java -jar picard.jar CreateSequenceDictionary R=hg38.fa O=hg38.dict
$ wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz
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