Professor, does it matter to have one flag before the other one? for example, in your code the --hwe was before the --maf flag. Does plink perform --hwe before --maf or everything is considered separately. You know professor that changing the position has different results if plink considers position.
Personally, I did not notice any changes, when I tried to flip the positions of quality control options. But overall, it could make a difference, in borderline cases. So in case, individuals are being removed due to poor data quality, it is worth doing the removal of poor quality SNPs first, to see if it helps to "save" some individual genotypes.
I am enjoying your work. But I am from Botany department. I am in trouble for fst value calc. For carrot samples. At end of directory , it show error in Manhattan CHR . Reply me.
Professor, I am sorry for the many questions, but I hope they make sense. First, I am wondering if it is mandatory to perform LD pruning before performing fst, second, when searching for signatures of selection, why is it necessary to confirm population structure? The third question, when searching for signatures of natural selection using integrated haplotype score (ihs) , does the procedure of QC for fst similar to ihs specifically checking for HWE and MAF. Lastly, how do we ensure we reduce the false discovery rate in this process? Thank you for your feedback.
Professor, does it matter to have one flag before the other one? for example, in your code the --hwe was before the --maf flag. Does plink perform --hwe before --maf or everything is considered separately. You know professor that changing the position has different results if plink considers position.
Personally, I did not notice any changes, when I tried to flip the positions of quality control options.
But overall, it could make a difference, in borderline cases. So in case, individuals are being removed due to poor data quality, it is worth doing the removal of poor quality SNPs first, to see if it helps to "save" some individual genotypes.
I am really enjoying your work and it helps a lot, keep up the good work and Thank you.
I am enjoying your work.
But I am from Botany department.
I am in trouble for fst value calc. For carrot samples.
At end of directory , it show error in Manhattan CHR .
Reply me.
are the carrots diploid? what is the error saying? did you set the appropriate chr count with the --chr-set option in PLINK?
Professor, I am sorry for the many questions, but I hope they make sense. First, I am wondering if it is mandatory to perform LD pruning before performing fst, second, when searching for signatures of selection, why is it necessary to confirm population structure? The third question, when searching for signatures of natural selection using integrated haplotype score (ihs) , does the procedure of QC for fst similar to ihs specifically checking for HWE and MAF. Lastly, how do we ensure we reduce the false discovery rate in this process? Thank you for your feedback.
Hi, did you found answers to your questions?