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) ?
REQUIRED for all errors and issues:
a) GATK version used:
The Genome Analysis Toolkit (GATK) v22.214.171.124
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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