GATK Germline CNV calling

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Krithika_Subramanian

• November 22, 2021 11:40

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: GATK-4.1.8.0
b) Exact command used: Followed this post workflow (https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants)
c) Entire error log:

I followed the above link Germline CNV calling workflow for our cohort samples. I am having a few doubts about the results. The below are my question:

1. In the output .vcf file, why only one sample name was reported for the INFO column of the header (attached screenshot)? Usually,population-level variant calling results have to provide each sample independently? 

2. How to calculate allele frequencies for our cohort result? 

 

 

Thank you,

Regards,

Krithika S

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  Krithika_Subramanian

  • November 22, 2021 12:00

  Attached screenshot

   

  

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  Pamela Bretscher

  • November 22, 2021 18:38

  Hi Krithika_Subramanian,

  I am going to move your post to the General Discussion section as the Germline section is for reporting bugs in GATK. However, it does appear that you may only be looking at the portion of the vcf file for this only sample and the other samples are likely present in the full vcf.

  Kind regards,

  Pamela 

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  Krithika_Subramanian

  • November 23, 2021 07:47

  Hi Pamela Bretscher,

  Thank you for moving this post to the general discussion. 

  After running "PostprocessGermlineCNVCalls" module which is the last step of this Germline CNV caller, it generates only one .vcf file (previously attached screenshot). There was no other full vcf file. Could you please give me more detail about this query?

   

  Thanks in advance

  Regards

  Krithika S

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  Muhammad Shoaib Akhtar

  • December 03, 2021 06:03

  Krithika_Subramanian can you please show the command which you ran at this stage?

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