Thanks for the tool. I am considering SNV calling from high throughput short read sequencing data of polyploid complex with the DeNovoGBS command.
Specifically 2x, 4x, 6x and individuals with unknown polyploidy level. Individuals with an unknown polyploidy level are 2x, 4x, or 6x and no other polyploidy levels are included. I am confused about setting the polyploidy level in the -ploidy option. Is it possible to call SNVs from polyploid complex data?
Best regards,
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Thanks for your interest in NGSEP. At this moment, our DeNovoGBS function does not have the functionality that you describe. We can add to the roadmap a feature to set the ploidy per sample. Now, guessing the ploidy from GBS data is a bit more tricky. You can start by running the DeNovoGBS, calculate the summary statistics and see if you can cluster the samples by the proportion of heterozygous sites. Although far from perfect, this could be a starting point.
Best regards
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello,
Thanks for the tool. I am considering SNV calling from high throughput short read sequencing data of polyploid complex with the DeNovoGBS command.
Specifically 2x, 4x, 6x and individuals with unknown polyploidy level. Individuals with an unknown polyploidy level are 2x, 4x, or 6x and no other polyploidy levels are included. I am confused about setting the polyploidy level in the -ploidy option. Is it possible to call SNVs from polyploid complex data?
Best regards,
Thanks for your interest in NGSEP. At this moment, our DeNovoGBS function does not have the functionality that you describe. We can add to the roadmap a feature to set the ploidy per sample. Now, guessing the ploidy from GBS data is a bit more tricky. You can start by running the DeNovoGBS, calculate the summary statistics and see if you can cluster the samples by the proportion of heterozygous sites. Although far from perfect, this could be a starting point.
Best regards