Common datasets for GATK

gatk_bundle_and_WGS_test_data.sh

#Known datasets: GATK bundle for human b37 reference
# 
wget -c ftp://[email protected]/bundle/b37/dbsnp_138.b37.vcf.gz.md5
wget -c ftp://[email protected]/bundle/b37/dbsnp_138.b37.vcf.gz
wget -c ftp://[email protected]/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz
wget -c ftp://[email protected]/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz.md5
wget -c ftp://[email protected]/bundle/b37/1000G_phase1.indels.b37.vcf.gz
wget -c ftp://[email protected]/bundle/b37/1000G_phase1.indels.b37.vcf.gz.md5
wget -c ftp://[email protected]/bundle/b37/1000G_phase1.snps.high_confidence.b37.vcf.gz
wget -c ftp://[email protected]/bundle/b37/1000G_phase1.snps.high_confidence.b37.vcf.gz.md5
wget -c ftp://[email protected]/bundle/b37/hapmap_3.3.b37.vcf.gz
wget -c ftp://[email protected]/bundle/b37/hapmap_3.3.b37.vcf.gz.md5
wget -c ftp://[email protected]/bundle/b37/1000G_omni2.5.b37.vcf.gz
wget -c ftp://[email protected]/bundle/b37/1000G_omni2.5.b37.vcf.gz.md5
wget -c ftp://[email protected]/bundle/b37/1000G_phase3_v4_20130502.sites.vcf.gz
wget -c ftp://[email protected]/bundle/b37/1000G_phase3_v4_20130502.sites.vcf.gz.md5

# human b37 reference: 使用的时候需要解压并建（bwa）比对的index
wget -c -O human_g1k_v37.fasta.gz ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz

## 创建bwa index
bwa index human_g1k_v37.fasta

# Get test fastq data: NA12878
wget -c -O NA12878_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR194/ERR194147/ERR194147_1.fastq.gz
wget -c -O NA12878_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR194/ERR194147/ERR194147_2.fastq.gz


## 外显子数据
wget -c -O NA12878-NGv3-LAB1360-A_1.fastq.gz https://s3.amazonaws.com/bcbio_nextgen/NA12878-NGv3-LAB1360-A_1.fastq.gz
wget -c -O NA12878-NGv3-LAB1360-A_2.fastq.gz https://s3.amazonaws.com/bcbio_nextgen/NA12878-NGv3-LAB1360-A_2.fastq.gz

这是外显子的区域文件，在GATK 进行变异检测那一步可以把 -L 的参数换成下面这个文件的区域就行，可以节省很多时间
wget -c -O NGv3.bed.gz https://s3.amazonaws.com/bcbio_nextgen/NGv3.bed.gz