TonyKess

joint genotyping optimal strategy

1

Working with a large-ish dataset (30TB raw reads), and was wondering what a good strategy would be for working with the joint_germline option to get cohort SNP calls. Would it...

joint germline vcftools error

9

### Description of the bug Joint germline genotyping completes actual genotyping, but fails at TSV count vcftools step ### Command used and terminal output Command: nextflow run nf-core/sarek --skip_tools baserecalibrator...

Index for non-model species

3

Hello, Wondering if it's possible to build indexes for quick genotyping of low coverage samples ( ~2-5x ~1500+) from a set of samples generated at higher coverage (~500, 10-20x) for...

Calculating RDA on large datasets

3

Hello, We're using the RDA function to carry out genome scans for signals of adaptation [similar to this paper](https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13722) - we are beginning to run into speed problems with very...