What is the best RadSeq/GBS pipeline in 2021?
Some of the tings that I am looking for in a GBS pipeline are:
- can be used with a reference genome
- automatic detection of enzyme / restriction sites used per sample (for the correct in-sillico digestion of the reference genome)
- can output standard BAM files
- can output GVCF files that can used together in GATK to do joint variant calling together with WGS GVCF files
Or is it maybe possible (with some tweaking of arguments and pre/post processing of data) to pull RadSeq/GBS data trough a BWA+GATK pipeline and still get good results?