Bcftools installed via Cygwin plugin error

[audreyrosemary]

Hi! I am trying to look at several genomes of different individuals of the same species and call the SNPs for each genome using bcftools. I installed bcftools via Cygwin terminal on Windows 10, but I keep receiving the following error when I am trying to use the plugins (count, etc.):

No functional bcftools plugins were found in
        BCFTOOLS_PLUGINS="/usr/local/libexec".

- Is the plugin path correct?

- Run "bcftools plugin -l" or "bcftools plugin -lvv" for a list of available plugins.

When I run "bcftools plugin -l" I get the same message. The original bcftools installation folder is in a different place compared to the installed bcftools that are in usr/local/libexec (the actual program is in usr/local/bin), so I tried to export the path to the plugins to the plugin folder in the original bcftools directory which didn't help. I also tried to leave the plugins path to "/usr/local/libexec" and manually copy-paste the plugins folder in there, but that issued again the error above. The plugins folder is in the path mentioned, but it is either not recognized or doesn't contain functional plugins. When I try to ask why does the count plugin specifically not work, I get the following message:

$ bcftools plugin count -vv
plugin directory /usr/local/libexec .. ok
/usr/local/libexec/count.cygdll:
        dlopen   .. No such file or directory
count:
        dlopen   .. No such file or directory

The bcftools plugin "count" was not found or is not functional in
        BCFTOOLS_PLUGINS="/usr/local/libexec".

- Is the plugin path correct?

- Run "bcftools plugin -l" or "bcftools plugin -lvv" for a list of available plugins.

Could not load "count".

The count.cygdll and count.c files do exist though in the plugins directory so I am confused of why the plugins are not recognized. I would deeply appreciate any input!

Furthermore, I would also appreciate any separate advice about how to align whole-genome assemblies to one reference genome in order to generate the required aligned .SAM file as input for bcftools. I know how to align short sequences, but I don't know for sure how to employ that for an entire genome.

Thank you very much!