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In README.md:

Indel maximum amount (Integer, 25-100): The maximum allowed indels in the .FASTA file, beyond the SNP location and 5 base pairs around it. Any indels found within a 2 base pair flanking of the SNP location will be automatically filtered out. Minimum indel threshold is 25%.

Could this be reworded so that it is clear that the "Indel maximum amount" is in units of percent, instead of base pairs or something similar. I suspect that you mean "Maximum percent of indel base pairs allowed within the full window size in base pairs." Also, is there a programatic reason why the minimum is 25% or a biological one?

In README.md it states that the maximum allowable window size is 99 base pairs.
However, in line 146 of SNPcontext, the code checks if the window size is above 10, and sets it to 10 if it is.
Additionally, the Zhu et al. 2017 paper uses a window size of 600 (300bp on both sides of the SNP).

We should consider what the maximum window size should be (10, 99, or larger), then implement and document the new value. It should also be clarified whether the window size extends to only one side of the SNP or covers both directions.

Could you add something like QUEUE= to the config file to allow users to control which queue the job is submitted to?

The README does not have any documentation describing how to call the program. It only lists the various options that are available in command-line mode.

For example:

To run SNP Context, use the following command:
./SNPcontext

If using a config file, use the following command:
./SNPcontext ~/path/to/your/context.config

A usage message for calling the program with a config file should also be added to the output from running ./SNPcontext with no arguments. Currently it only describes the command-line mode.