GBS SNPs calling

Question

[shinken123]

Hi all,

I am wondering if you could recommend me a pipeline to call SNPs from GBS data.

I see two principal alternatives:

1.- Demultiplexing, filter raw reads, mapping to a reference genome, preprocessing the alignment files, and call SNPs with GATK or samtools or other sofware.

2.- Use TASSEL or FAST-GBS or another software designed for this.

I am wondering if some one have experience with these two approaches. Call SNPs carrying all the steps such as in WGS or use a special pipeline for GBS. Which is better?

[shinken123]

Thank you, the paper was really helpful.

Answer 1

[reza.jabal]

Have you read this paper? https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2827-7

Answer 2

[Arthur Melo]

GBS-SNP-CROP: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-0879-y https://github.com/halelab/GBS-SNP-CROP

Answer 3

[rimgubaev]

For me TASSEL-GBS works faster and I would recommend it. If you to use GATK for GBS/RAD-seq it will require additional steps and modify the pipeline. Here you can see such example and try to adapt it for your needs.