In the readme you need '-T' as obligatory paramater to run KIN (although down at the option description it is missing. So I tought we need to provide the targets file just as at data preparation to select which samples we want to analyze).
However this parameter is not existing and not needed at KIN. It only exists in KINgaroo.
The tool '-h' option is OK, the only miskleading thing was that I read the README for parameters.
As a side note, a step by step tutorial from the beginning with describing the expectations on data, and the limitations/pitfalls, the actual commands to preparate data, some toughts on the markerset, whether 1240K SNP file is suitable for the analysis, if any other step is required to thin the marker set for LD markers etc would be nice.
Just a minor comment.
In the readme you need '-T' as obligatory paramater to run KIN (although down at the option description it is missing. So I tought we need to provide the targets file just as at data preparation to select which samples we want to analyze).
However this parameter is not existing and not needed at KIN. It only exists in KINgaroo.
The tool '-h' option is OK, the only miskleading thing was that I read the README for parameters.
As a side note, a step by step tutorial from the beginning with describing the expectations on data, and the limitations/pitfalls, the actual commands to preparate data, some toughts on the markerset, whether 1240K SNP file is suitable for the analysis, if any other step is required to thin the marker set for LD markers etc would be nice.
Regards, Zoltan