Hi, we have encountered some problems with counting the number of heterozygous sites at the final step of MoChA (Version 1.14-20220112).
Take chr1 as an example, when we combined all samples (~450,000) in one bcf file for analysis, only about ten heterozygous sites can be counted (as shown in the n_hets column) and used for the following analyses. However, the number of n_hets increases greatly when we split the combined bcf file and included only 10,000 samples or even 100 samples for analysis.
I cannot figure out the problem, and there is no error message. Could you please give me some suggestions for dealing with this?
Hi, we have encountered some problems with counting the number of heterozygous sites at the final step of MoChA (Version 1.14-20220112).
Take chr1 as an example, when we combined all samples (~450,000) in one bcf file for analysis, only about ten heterozygous sites can be counted (as shown in the n_hets column) and used for the following analyses. However, the number of n_hets increases greatly when we split the combined bcf file and included only 10,000 samples or even 100 samples for analysis.
I cannot figure out the problem, and there is no error message. Could you please give me some suggestions for dealing with this?
Thanks.