Can Monopogen use for calling variants in Malaria parasite single cell Data ?

KChen-lab / Monopogen

SNV calling from single cell sequencing

GNU General Public License v3.0

68 stars 16 forks source link

Can Monopogen use for calling variants in Malaria parasite single cell Data ? #39

Closed MJBioInfo closed 4 months ago

MJBioInfo commented 5 months ago

Dear Monopogen developers , Is it possible to call variants on single cell data from Malaria parasite ? If yes How LD works . DO we need to prepare some files ?

your valuable suggestions is greatly appreciated

jinzhuangdou commented 5 months ago

Unfortunately monopogen only works on human genomics data. The LD is constructed on 1KG3 population panel.

xinghua1001 commented 5 months ago

Hi Dr. Dou, If I have some population genetic data for my species (more than 100 individuals), can I use it for monopogen on this species?

jinzhuangdou commented 5 months ago

Yes, you can build your own reference panel (similar with 1KG3) and then run Monopogen. Maybe you can follow beagle manual (http://faculty.washington.edu/browning/beagle/beagle.html).