基因组序列及注释数据下载

1. 网站下载

NCBI   Download - NCBI

Ensembl  Accessing Ensembl Data

UCSC   https://hgdownload.soe.ucsc.edu/downloads.html

2. 命令行下载 

从ucsc下载基因组序列

wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz ./
wget  https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/md5sum.txt ./

wget https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz ./
wget https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/md5sum.txt ./

从Ensemble下载注释数据

wget http://ftp.ensembl.org/pub/release 104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz ./

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下载annovar 注释数据

# datadb list from annovar
annotate_variation.pl -downdb -webfrom annovar avdblist humandb/ -buildver hg38

wget http://www.openbioinformatics.org/annovar/download/hg38_avdblist.txt.gz ./

Broadinstitute GATK数据下载

ftp 
open ftp.broadinstitute.org  # 连接站点
# 输入用户名
gsapubftp-anonymous
# 密码 直接回车
# 查看文件，切换目录
ls 
cd  

close # 关闭连接
exit #推出ftp

nohup wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/* .  &
nohup wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg19/* .  &
nohup wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/Mutect2/* .  &
nohup wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/oncotator/* .  &
nohup wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/* . &

Reference：

参考基因组及注释文件下载 - 小xuo生 - 博客园

Ensembl 基因组下载方法-新闻-诺禾致源

ENSEMBL | 生信菜鸟团