unable to create contig_ploidy_model

Follow

Vishal Mishra

• February 20, 2020 06:23

Hii Team,

I am using latest version of GATK.

I have single exome file and i want cnv analysis.

Process:-

1) PreProcessInterval

2) CollectReadCounts

3) AnnotateInterval (Optional)

4) DetermineGermlineContigPloidy

 

Now can anyone please suggest me how to generate or create contig_ploidy_model for DetermineGermlineContigPloidy.

 

1

• 

  Derek Caetano-Anolles

  • February 24, 2020 15:00

  Here is a description of how to use DetermineGermlineContigPloidy and GermlineCNVCaller to do the type of CNV analyses you are looking for. If you need more information, the DetermineGermlineContigPloidy tool documentation is here.

  2

  Comment actions Permalink
• 

  Vishal Mishra

  • February 25, 2020 06:39

  Thanks for reply.

   

  I have exome data to do cnv analysis. Can you please suggest me the command for single sample and i am not using DetermineGermlineContigPloidy Beta version.

   

  1

  Comment actions Permalink
• 

  Andrey Smirnov

  • February 25, 2020 17:05

  Vishal Mishra  You cannot analyze a single exome with GATK gCNV. For running GATK Germline CNV pipeline you will need to first learn a gCNV "ploidy model" and "denoising model" using a cohort of samples. Later, you can use that model to make calls on individual samples. Please see this document for you reference: https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variant

  1

  Comment actions Permalink

Please sign in to leave a comment.