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Identify haploid vs. diploid samples
Hello! I have RNAseq data from 40 insects with a haplodiploid sex determination system. While for pupae and adults I know the sex of the individuals, I would like to determine the sex of the younger life stages. I believe there should be a way to use SNP variants to determine whether a particular library is from a haploid (male) or diploid (female) individual, but I don't know how the GATK tools work and what would be most appropriate. I would appreciate any advice!