af-only-gnomad.vcf.gz for hg19

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chenglei

• November 18, 2021 14:00

where could I find af-only-gnomad.vcf.gz for hg19, I just found af-only-gnomad.vcf.gz for hg38, I check https://console.cloud.google.com/storage/browser/gcp-public-data--broad-references/hg19/v0;tab=objects?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&prefix=&forceOnObjectsSortingFiltering=false and https://console.cloud.google.com/storage/browser/gatk-best-practices?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&prefix=&forceOnObjectsSortingFiltering=false , and https://console.cloud.google.com/storage/browser/genomics-public-data?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&prefix=&forceOnObjectsSortingFiltering=true  ,but I did not find af-only-gnomad.vcf.gz for hg19, could someone provide a link where I can download the file af-only-gnomad.vcf.gz for hg19? Appreciate！

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• 

  Genevieve Brandt (she/her)

  • November 24, 2021 21:05

  Hi chenglei,

  I don't have the availability to search through our resource bundle and see if it is available, but here is the link to our resource bundle: https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle

  You can look through there to see if there are any locations you haven't checked yet. 

  Best,

  Genevieve

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• 

  Elena S Kim

  • November 06, 2024 17:25

  Hello everyone, I know it is an old thread, but for those who stubled upon this in desperate search of the files,  I wanted to share where I finally found the legacy hg19 files I needed:

  gsutil ls gs://gatk-best-practices/somatic-b37/

  gs://gatk-best-practices/somatic-b37/

  gs://gatk-best-practices/somatic-b37/CNV.hg19.bypos.v1.CR1_event_added.mod.seg

  gs://gatk-best-practices/somatic-b37/CNV_and_centromere_blacklist.hg19.list

  gs://gatk-best-practices/somatic-b37/HCC1143.bai

  gs://gatk-best-practices/somatic-b37/HCC1143.bam

  gs://gatk-best-practices/somatic-b37/HCC1143_normal.bai

  gs://gatk-best-practices/somatic-b37/HCC1143_normal.bam

  gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.dict

  gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta

  gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta.fai

  gs://gatk-best-practices/somatic-b37/Mutect2-WGS-panel-b37.vcf

  gs://gatk-best-practices/somatic-b37/Mutect2-WGS-panel-b37.vcf.idx

  gs://gatk-best-practices/somatic-b37/Mutect2-exome-panel.vcf

  gs://gatk-best-practices/somatic-b37/Mutect2-exome-panel.vcf.idx

  gs://gatk-best-practices/somatic-b37/README.txt

  gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf

  gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf.idx

  gs://gatk-best-practices/somatic-b37/final_centromere_hg19.seg

  gs://gatk-best-practices/somatic-b37/onco_config.txt

  gs://gatk-best-practices/somatic-b37/oncotator_v1_ds_April052016.tar.gz

  gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf

  gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf.idx

  gs://gatk-best-practices/somatic-b37/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval_list

  gs://gatk-best-practices/somatic-b37/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list

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