gatk 对多倍体的支持 ploidy 参数
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https://gatk.broadinstitute.org/hc/en-us/articles/360035889691-Does-GATK-work-on-non-diploid-organisms-
Cases where ploidy needs to be specified
Native variant calling in haploid or polyploid organisms.
Pooled calling where many pooled organisms share a single barcode and hence are treated as a single "sample".
Pooled validation/genotyping at known sites.
For normal organism ploidy, you just set the -ploidy argument to the desired number of chromosomes per organism. In the case of pooled sequencing experiments, this argument should be set to the number of chromosomes per barcoded sample, i.e. (Ploidy per individual) * (Individuals in pool). -
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03704-1
Evaluation of variant calling tools for large plant genome re-sequencing