Searching for tool to assign data as haploid or diploid
Hi!
I have a large data set (180 WGS individuals) of honey bees larvae. However, the way these samples were collected means we have no information on if we can expect these sequences to be haploid or diploid. I am searching for a way to easily (and computationally light-ish if possible) assign their ploidy. I've been thinking of perhaps subsampling and only using one chromosome of each individual to investigate variants, but am open to other (better) ideas, or if there is already a tool out there that would be great.
Thanks!
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I looked into that tool, but it seems to only look at diploid and higher ploidy, it doesn't mention haploploidy, or how it handles that. Did find two other tools via this tool HMMploidy and ploidyNGS that seem to be able to handle haploid data. So will try it out on my data :) Thanks!
So the data is in form of set of 180 sample files i.e. there was no pooling of any sort.
Yes, no pooling at all, I have a little over 180 individual bam files