I am using "switch" tool to compute SER. In the documentation, there are three usages of the tool and I am following the "Benchmark haplotypes using simulated data".
My validation data has 36 samples, while the estimation data (phased data) has 103 samples. 36 samples from validation data matches with the subset of 103 samples of phased data, but I am not able to get any SER. I have no information in data.phased.sample.switch.txt.gz file and for data.phased.variant.switch.txt.gz, SER for each variant seems "-nan", which I don't know what it stands for.
The validation data I use is not simulated data, it is a previously phased data of the same Drosophila simulans population. I thought I can change the sample names of the validation data and match it with the subset of my phased samples, but apparently this is not working.
I am not sure about what not having SER means, does that mean everything went well and there is no SER? Or is there something wrong I am doing with the validation data?
I would be appreciate if you can help me regarding this.
Best regards,
Bilge
Hi,
I am using "switch" tool to compute SER. In the documentation, there are three usages of the tool and I am following the "Benchmark haplotypes using simulated data".
My validation data has 36 samples, while the estimation data (phased data) has 103 samples. 36 samples from validation data matches with the subset of 103 samples of phased data, but I am not able to get any SER. I have no information in data.phased.sample.switch.txt.gz file and for data.phased.variant.switch.txt.gz, SER for each variant seems "-nan", which I don't know what it stands for.
The validation data I use is not simulated data, it is a previously phased data of the same Drosophila simulans population. I thought I can change the sample names of the validation data and match it with the subset of my phased samples, but apparently this is not working.
I am not sure about what not having SER means, does that mean everything went well and there is no SER? Or is there something wrong I am doing with the validation data?
I would be appreciate if you can help me regarding this. Best regards, Bilge