GBS SNPs calling
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5.6 years ago
shinken123 ▴ 110

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 • 3.4k views
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Thank you, the paper was really helpful.

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7 months ago
rimgubaev ▴ 300

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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