GenotypeGvcf tetraploids as diploids

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julien leuenberger

• August 12, 2022 09:26

Hi,

I'm working with tetraploids potato gbs datas. I have a little issue actually I've done all steps before genotypeGvcfs as tetraploids but I want to try to perform the genotype calling (multisample .g.vcf) as a diploid organism (so I will just have aa:ab:bb instead of aaaa:aaab:aabb:abbb:bbbb). The problem is when I use --sample-ploidy 2 the final vcf is still as tetraploid. Does it possible to change something or I have to redo all the pipeline from haplotypecaller (which is quite long) ?

 

Cheers,

Julien Leuenberger

 

 

 

REQUIRED for all errors and issues:
a) GATK version used:

The Genome Analysis Toolkit (GATK) v4.2.6.1
b) Exact command used:

gatk GenotypeGVCFs -V combined_4x_DMv6_chr11.g.vcf -O test_2x_chr4.vcf --sample-ploidy 2 -R ../../reference_v6/DM_1-3_516_R44_potato_genome_assembly.v6.1.fasta

 

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  Genevieve Brandt (she/her)

  • August 18, 2022 18:22

  Hi julien leuenberger,

  What was the --sample-ploidy option you used for HaplotypeCaller?

  Best,

  Genevieve

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  julien leuenberger

  • August 19, 2022 07:41

  Hi

  thanks for answering. The ploidy use for haplotype caller depand of the sample most part is 4 and some sample are 2. 

   

  Cheers,

  Julien

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  Genevieve Brandt (she/her)

  • August 19, 2022 20:55

  Hi Julien,

  I believe you should get consistent results if you keep the ploidy consistent between HaplotypeCaller and GenotypeGVCFs.

  Best,

  Genevieve

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  julien leuenberger

  • August 21, 2022 22:00

  Ok thanks enjoy your day,

  cheers,

  julien

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