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stschiff / msmc2

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Haploid problem #53

Open cfz1998 opened 1 year ago

cfz1998 commented 1 year ago

Hi! @stschiff

Does MSMC2 work for haploid? My organisms is haploid.

Thank you for your reply! --CFZ

stschiff commented 1 year ago

Yes, if it is recombining. If not, then you don't need MSMC, you can just use any phylogenetic software or build a neighbour-joining tree.

cfz1998 commented 1 year ago

Hi！@stschiff
Should make a “pseudo-diploid”(merge two sample genotypes) after bamCaller.py? Or just simply double each sample genotype and pick only one haplotype to msmc2? Like: msmc2 -t 40 -p 1*2+25*1+1*2 -i 100 -I 0,2,4,6,8,10,12,14 8 samples

--CFZ

cfz1998 commented 1 year ago

And, if merged two Haploid samples to a “pseudo-diploid”. How to deal with the “mask.bed.gz” from bamCaller.py? Simply merged(Interval merging) the “mask.bed.gz” from two Haploid samples?