Hi,
Thanks for developing GADMA. I am new to demographic analysis and am struggling to understand the "effective length of sequence" required in the parameter file.
I have read the FAQ, but I want to make sure I’ve interpreted it correctly. For whole genome sequencing, does 'Nseq' refer to the total genome length, or is it the average read size obtained from a BAM file for paired-end data? (I have seen in the issue section average read length * number of SNPs)
If I use ANGSD to call likelihood scores with standard filtering parameters, what do X and Y represent? Additionally, can X ever equal Y in this context?
It would be very helpful if the FAQ included examples for different scenarios or data types. I have seen various examples in the GitHub issues, which has left me quite confused.
Best regards,
Shri
Hi,
Thanks for developing GADMA. I am new to demographic analysis and am struggling to understand the "effective length of sequence" required in the parameter file.
I have read the FAQ, but I want to make sure I’ve interpreted it correctly. For whole genome sequencing, does 'Nseq' refer to the total genome length, or is it the average read size obtained from a BAM file for paired-end data? (I have seen in the issue section average read length * number of SNPs)
If I use ANGSD to call likelihood scores with standard filtering parameters, what do X and Y represent? Additionally, can X ever equal Y in this context?
It would be very helpful if the FAQ included examples for different scenarios or data types. I have seen various examples in the GitHub issues, which has left me quite confused.
Best regards,
Shri