Comments (5)
Oh I see what you mean. The diploid false option is really for polyploid genomes or non-colonal samples (cancer samples etc) rather than haploid. Using the diplod false option on a haploid genome will probably result in worse performance as some features will not be used in the machine learning classifier. I recommend using diploid true, even for a haploid genome. With regard to the 0/1 genotype, this can happen at some sites if there are ambiguous mappings. There is no option to force a haploid genotype call. If you know your sample is haploid, you can ignore these or change them to haploid genotype
Thanks Kez!
Best.
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Hi @wushyer,
Yes, it should work even better than diploid.
from dysgu.
Hi @wushyer, Yes, it should work even better than diploid.
Thanks for the quick relpy. That's very good to know!
Best,
Shuangyang
from dysgu.
Hi Kez,
If I understand the tools correctly, I only need to set '--diploid FALSE' is enough for non-diploid species. Is that right? Thanks.
By the way, I have run it and get the genotype as '0/1', how do I understand this label? My species is haploid genome.
Best
Shuangyang
from dysgu.
Oh I see what you mean. The diploid false option is really for polyploid genomes or non-colonal samples (cancer samples etc) rather than haploid. Using the diplod false option on a haploid genome will probably result in worse performance as some features will not be used in the machine learning classifier. I recommend using diploid true, even for a haploid genome. With regard to the 0/1 genotype, this can happen at some sites if there are ambiguous mappings. There is no option to force a haploid genotype call. If you know your sample is haploid, you can ignore these or change them to haploid genotype
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