DetermineGermlineContigPloidy

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faramarzg

• October 19, 2021 15:44

GATK version used: 4.2.2.0

Hello dear supporter

How do I generate contig ploidy table for --contig-ploidy-priors option in DetermineGermlineContigPloidy tool?

This is very confusing for me. I searched for several days in various databases and contents provided by GATK topics, but I did not find any idea. please guide me... . What tools and instructions should I use to create this table?

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• 

  Emil Furat

  • November 04, 2021 18:06
  • Edited

  Hi faramarzg,

   

  I believe that the documentation you are looking for is the following: https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants. Please refer to step (3) for more information about using DetermineGermlineContigPloidy.

   

  Are you trying to use DetermineGermlineContigPloidy in cohort mode or in case mode? 

   

  If you have any other questions please let us know.

   

  Kind regards,

  Emil

   

   

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  faramarzg

  • November 09, 2021 00:17

  I was confused to that What is the appropriate input for  --contig-ploidy-priors option.

  I generate this file manually. Any user can do this as following:

  ==> open Excel and put values in correct cell (shown in picture) > save this file as tab delimited text file > manually change file format from contig_ploidy_table.txt to contig_ploidy_table.tsv  .

   

  This file provided to use for Human genome. If your genome reference file does not containing mitochondrial sequence, so, purge last row.

   

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  Emil Furat

  • November 10, 2021 18:35

  Hi faramarzg,

   

  We appreciate you taking the time to explain your solution to this issue!

  If you have any other questions please let us know.

   

  Kind regards,

  Emil

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