GATK GenotypeGVCFs --sample-ploidy

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lizhichao

• January 19, 2022 04:06

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used:GATK 4.1.2
b) Exact command used: GATK GenotypeGVCFs --sample-ploidy 
c) Entire error log:

If not an error, choose a category for your question(REQUIRED):
a)How do I set the --sample-ploidy  param when I running joint-calling with 1000 samples , the default 2,or 1000*2 or some else?

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• Official comment

  

  Genevieve Brandt (she/her)

  • January 21, 2022 00:01

  Hi lizhichao,

  The --sample-ploidy argument should be set to be the number of chromosomes per sample. So if each sample has 2 chromosomes, then the --sample-ploidy would be 2. 

  You can read more here:  https://gatk.broadinstitute.org/hc/en-us/articles/4414594430619-GenotypeGVCFs#--sample-ploidy

  Please let me know if you have other questions.

  Best,

  Genevieve

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  Genevieve Brandt (she/her)

  • January 19, 2022 20:16

  Hi lizhichao,

  I am going to move your post into our Community Discussions -> General Discussion topic, as the Germline 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

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