Forked from ShujiaHuang/gatk_bundle_and_WGS_test_data.sh
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April 1, 2019 15:33
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Common datasets for GATK
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| #Known datasets: GATK bundle for human b37 reference | |
| # | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/dbsnp_138.b37.vcf.gz.md5 | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/dbsnp_138.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz.md5 | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.indels.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.indels.b37.vcf.gz.md5 | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.snps.high_confidence.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.snps.high_confidence.b37.vcf.gz.md5 | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/hapmap_3.3.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/hapmap_3.3.b37.vcf.gz.md5 | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_omni2.5.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_omni2.5.b37.vcf.gz.md5 | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase3_v4_20130502.sites.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/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 | |
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#Known datasets: GATK bundle for human b37 reference
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/dbsnp_138.b37.vcf.gz.md5
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/dbsnp_138.b37.vcf.gz
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz.md5
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.indels.b37.vcf.gz
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.indels.b37.vcf.gz.md5
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.snps.high_confidence.b37.vcf.gz
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.snps.high_confidence.b37.vcf.gz.md5
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/hapmap_3.3.b37.vcf.gz
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/hapmap_3.3.b37.vcf.gz.md5
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_omni2.5.b37.vcf.gz
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_omni2.5.b37.vcf.gz.md5
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase3_v4_20130502.sites.vcf.gz
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase3_v4_20130502.sites.vcf.gz.md5
human b37 reference: Need to decompress and build (bwa) the index of the comparison
wget -c -O human_g1k_v37.fasta.gz ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz
Create 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
Exon data
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
This is the region file of the exon. In GATK, the mutation detection step can replace the -L parameter with the area of the following file,
which can save a lot of time.
wget -c -O NGv3.bed.gz https://s3.amazonaws.com/bcbio_nextgen/NGv3.bed.gz