hunman参考基因组下载及索引建立

进入UCSC官网，

进入hunman基因组页面，点击基因组数据，

下载hg38.analysisSet.2bit

wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/hg38.analysisSet.2bit

下载UCSC工具包，将2bit格式的参考基因组转为fasta格式

rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/ ./

./twoBitToFa hg38.analysisSet.2bit hg38.fa

建立samtools索引：

#samtools_faidx.sh
./samtools faidx hg38.fa

建立BWA索引

#bwa_index.sh
bwa index -a bwtsw hg38.fa

下载picard工具包
http://broadinstitute.github.io/picard/

wget https://github.com/broadinstitute/picard/releases/download/2.23.0/picard.jar

对hg38.fa建立索引

java -jar picard.jar CreateSequenceDictionary R=hg38.fa O=hg38.dict