somatic CNV PoN recommendation?

Answered

Follow

Qing Zhang

• August 05, 2021 18:17

is there a recommended source of somatic CNV PoN that works with the latest GATK?

(I know I can build my own, but just wonder if one from a larger cohort already exists)

0

• 

  Pamela Bretscher

  • August 05, 2021 19:02

  Hi Qing Zhang,

  There are public PoN resources available in the Resource Bundle also referenced in this article about the Panel of Normals. Does this help answer your question?

  Kind regards,

  Pamela

  0

  Comment actions Permalink
• 

  Qing Zhang

  • August 05, 2021 19:06

  Hi,

  I want hg38 CNV PoN, not SNV. Is there a public CNV PoN for somatic analysis?

  0

  Comment actions Permalink
• 

  Pamela Bretscher

  • August 05, 2021 19:37

  Hi Qing Zhang,

  All of the available public resources offered by GATK are located in the Resource Bundle. If what you are looking for is not present there, then it is not offered directly from GATK, but you may be able to find resources by searching old forum posts or from input by other users. 

  Kind regards,

  Pamela

  0

  Comment actions Permalink
• 

  Ibel Carri

  • April 06, 2022 18:48

  Hi, I found this file in the resource bundle https://storage.googleapis.com/gatk-test-data/cnv/somatic/wes-do-gc.pon.hdf5

  0

  Comment actions Permalink
• 

  Genevieve Brandt (she/her)

  • April 07, 2022 18:17

  Thank you for posting this resource Ibel Carri!

  0

  Comment actions Permalink

Please sign in to leave a comment.