Best (GATK compatible) RadSeq/GBS pipeline in 2021

Question

[William]

What is the best RadSeq/GBS pipeline in 2021?

Some of the tings that I am looking for in a GBS pipeline are:

1. can be used with a reference genome
2. automatic detection of enzyme / restriction sites used per sample (for the correct in-sillico digestion of the reference genome)
3. can output standard BAM files
4. 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?

Thank you.

[William]

Just processing RadSeq/GBS as 'faulty' WGS data did not seem to work. This results is c.a. 33% less TruePositive HOM_VAR SNPs, compared to a dedicated RadSeq/GBS pipeline and a benchmark WGS sample. So these RadSeq/GBS pipelines do do something useful to achieve better variant calling results. . My main guess is in-silico digestion of the reference genome with the relevant restriction enzyme.
Still am interested in a RadSeq/GBS pipeline that can output GATK compatible GVCF files.

Answer 1

[rimgubaev]

I persannoly tried two pipelines to do so. The first one is based on the GATK that use reference genome, however you need to work with you data with additional tools like axe-demux. Here you can find a modified scripts to to perform such calling with GATK. Later I tried TASSEL-GBS for me it worked faster (also with reference) as it is adapted for GBS/RAD-seq data and you set your restriction sites.