Question: GBS SNPs calling
0
gravatar for shinken123
2.4 years 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 12 months ago by Arthur Melo0 • written 2.4 years ago by shinken12380
1

Thank you, the paper was really helpful.

ADD REPLYlink written 2.4 years ago by shinken12380
1
gravatar for reza.jabal
2.4 years ago by
reza.jabal330
New York, USA
reza.jabal330 wrote:

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

ADD COMMENTlink written 2.4 years ago by reza.jabal330
0
gravatar for Arthur Melo
12 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 12 months ago by Arthur Melo0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1046 users visited in the last hour