2 下载GATK需要的参考基因组文件

参考基因组及必备的数据库

参考基因组下载

我是从服务器上下载下来放本地电脑了

下载方式1：

直接去gatk官网下载，下载链接为ftp://ftp.broadinstitute.org/bundle/

image.png

下载方式2：也是官网，但通过ftp匿名登录下载

location: ftp.broadinstitute.org/bundle
username: gsapubftp-anonymous
password:

3下载后的hg38的bwa_index文件夹内有以下文件：

kelly@DESKTOP-MRA1M1F:/mnt/f/kelly/bioTree/server/wesproject/hg38$ tree -h
.
├── [1.8G]  1000G_phase1.snps.high_confidence.hg38.vcf.gz
├── [2.0M]  1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi
├── [4.0K]  bwa_index
│   ├── [ 20K]  gatk_hg38.amb
│   ├── [445K]  gatk_hg38.ann
│   ├── [3.0G]  gatk_hg38.bwt
│   ├── [767M]  gatk_hg38.pac
│   ├── [1.5G]  gatk_hg38.sa
│   ├── [6.2K]  hg38.bwa_index.log
│   ├── [   0]  index.129248.err
│   ├── [   0]  index.129248.out
│   └── [ 566]  run.sh
├── [4.0K]  cnv
│   ├── [5.8M]  hg38.chr.bed
│   ├── [6.7M]  list.interval_list
│   ├── [ 843]  readme.txt
│   └── [5.7M]  targets.preprocessed.interval.list
├── [3.2G]  dbsnp_146.hg38.vcf.gz
├── [3.0M]  dbsnp_146.hg38.vcf.gz.tbi
├── [ 59M]  hapmap_3.3.hg38.vcf.gz
├── [1.5M]  hapmap_3.3.hg38.vcf.gz.tbi
├── [568K]  Homo_sapiens_assembly38.dict
├── [3.0G]  Homo_sapiens_assembly38.fasta
├── [157K]  Homo_sapiens_assembly38.fasta.fai
├── [ 20M]  Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
├── [1.4M]  Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi
└── [1018]  run.sh