About the accessibility of gnomad.genomes.v3.1.1.sites.vcf.bgz for mutect2 somatic mutation calling

Answered

Follow

Li Liu

• May 13, 2021 13:50

Dear GATK team,

I'm Li, a junior researcher currently working on using mutect2 for calling somatic mutation. I used hg38 as the reference genome and I heard gnomAD has recently released the latest version of v3.1.1 genome file. However, when I visit the google bucket of gnomAD v3.1.1: https://console.cloud.google.com/storage/browser/gcp-public-data--gnomad/release/3.1.1/vcf/genomes/ ,it doesn't seem there is an intact file named gnomad.genomes.v3.1.1.sites.vcf.bgz, unlike the gnomad.genomes.r2.1.1.sites.vcf.bgz from https://console.cloud.google.com/storage/browser/gcp-public-data--gnomad/release/2.1.1/vcf/ for hg19. 

I wonder if it’s possible to access the intact gnomad.genomes.v3.1.1.sites.vcf.bgz for my current research? Or when this file will be accessible to the public?

Thanks for your help.

Best regards,

Li

0

• 

  Genevieve Brandt (she/her)

  • May 13, 2021 16:13

  Hi Li,

  I am going to move your post into our Community Discussions -> General Discussion topic, as the Somatic topic is for reporting bugs and issues with GATK.

  You can read more about our forum guidelines and the topics here: Forum Guidelines.

  Best,

  Genevieve

  1

  Comment actions Permalink
• 

  Genevieve Brandt (she/her)

  • May 27, 2021 15:37

  Hi Li Liu,

  It looks like the files are available but they are separated by chromosome. Are you just looking for a combined version of these files? 

  If so, I'm not sure that is in the plan as of now, but if a big group of users would like to see a different file type, then it would be possible to make a request.

  Best,

  Genevieve

  0

  Comment actions Permalink

Please sign in to leave a comment.