The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
Leishmania has 36 chromosomes but their copy number is unpredictable for each strain and chromosome copy number can change very quickly. So what is an optimal ploidy setting for organisms with extensive aneuploidy? So far we use just diploid setting. Some samples have consistently more heterozygous SNPs in higher copy chromosomes but this relationship does not hold in many other samples: there is no strong correlation between chromosome copy number and abundance of heterozygous SNPs.