gatk4的一些介绍

gatk4的一些介绍

#GENOME
wget -t 0 -c https://storage.cloud.google.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta &
wget -t 0 -c https://storage.cloud.google.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.fai &
wget -t 0 -c https://storage.cloud.google.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dict &

#BWA index
cd /home/lzn/WES/genome/index
wget -t 0 -c https://storage.cloud.google.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb &
wget -t 0 -c https://storage.cloud.google.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann &
wget -t 0 -c https://storage.cloud.google.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt &
wget -t 0 -c https://storage.cloud.google.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac &
wget -t 0 -c https://storage.cloud.google.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa &

#SNP&INDEL
wget -t 0 -c https://storage.cloud.google.com/genomics-public-data/resources/broad/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz &
wget -t 0 -c https://storage.cloud.google.com/genomics-public-data/resources/broad/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi &
wget -t 0 -c https://storage.cloud.google.com/genomics-public-data/resources/broad/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz &
wget -t 0 -c https://storage.cloud.google.com/genomics-public-data/resources/broad/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi &
https://www.jianshu.com/p/155882b3005a
https://www.plob.org/article/7005.html
注意，需要下载100G的必备数据才能使用GATK。
https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4

https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle
ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/