gatk legacy bundles (where to get Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz)

Question

[nkinney06]

I need the known indels vcf to run gatk BaseRecalibrator. So I need hg19 (not the b37) version of the known indels: Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz

However this file is no longer available at: ftp://[e-mail]/bundle/hg19/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz

the broad institute documentation says the ftp site was disabled last year (https://gatk.broadinstitute.org/hc/en-us/articles/360035890811) so I checked the gcp bucket using the following command: gsutil ls gs://gatk-legacy-bundles/hg19/

output:

gs://gatk-legacy-bundles/hg19/
gs://gatk-legacy-bundles/hg19/ucsc.hg19.dict
gs://gatk-legacy-bundles/hg19/ucsc.hg19.fasta
gs://gatk-legacy-bundles/hg19/ucsc.hg19.fasta.fai

In other words, I cant find Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz in the gatk-legacy-bundles bucket. Does anyone know where this file is now available for download?

[GenoMax]

The files are available in this bucket.

[nkinney06]

Thanks but those are all hg38 not hg19. I know about liftover tools but the file I need should still be available

[GenoMax]

Your best bet may be to ask GATK support. hg19 version does not seem to be readily available via a search.

[Edmond]

These files are for hg38, not hg19. Do you know were are the files for hg19 ?

[GenoMax]

Please ask GATK support via their forum and then come back to provide that information here for future visitors.

Answer 1

[ning]

You can find the legacy bundle at their ftp site, but you have to be logged in as gsapubftp-anonymous (logging in as anonymous will not show the bundle).

ShujiaHuang on GitHub provides some wget commands to retrieve those files:

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

view raw gatk_bundle_and_WGS_test_data.sh hosted with ❤ by GitHub

[Ishak]

thanks soooooo much