Day 9_2 ESCC WES实战

需要有的东西

/public/biosoft/GATK/resources/bundle/hg38/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 
`-- [ 566]  run.sh

/public/biosoft/GATK/resources/bundle/hg38/
|-- [1.8G]  1000G_phase1.snps.high_confidence.hg38.vcf.gz
|-- [2.0M]  1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi
|-- [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

作者：生信技能树
链接：https://www.jianshu.com/p/49d035b121b8
來源：
著作权归作者所有，任何形式的转载都请联系作者获得授权并注明出处。

肿瘤分析流程GATK网址

肿瘤分析流程GATK

下载这篇文章的数据：Genomic comparison of esophageal squamous cell carcinoma and its precursor lesions by multi-region whole-exome sequencing

step 1 搜索数据下载

all database下搜索

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