Question: GBS SNPs calling
0
gravatar for shinken123
24 months ago by
shinken12380
México
shinken12380 wrote:

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?

ADD COMMENTlink modified 7 months ago by Arthur Melo0 • written 24 months ago by shinken12380
1

Thank you, the paper was really helpful.

ADD REPLYlink written 24 months ago by shinken12380
1
gravatar for reza.jabal
24 months ago by
reza.jabal300
United Kingdom
reza.jabal300 wrote:

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

ADD COMMENTlink written 24 months ago by reza.jabal300
0
gravatar for Arthur Melo
7 months ago by
Brazil
Arthur Melo0 wrote:

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

ADD COMMENTlink written 7 months ago by Arthur Melo0
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