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GBS SNPs calling

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?

gbs samtools gatk fast-gbs snp calling
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updated by rimgubaev rimgubaev • written by shinken123 shinken123

Thank you, the paper was really helpful.

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written by shinken123 shinken123

3 answers

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

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written by reza.jabal reza.jabal

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.

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written by rimgubaev rimgubaev

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