How used the best SNP calling workflow for GBS or full genome sequencing !!!!

From fastq to bam 

RattleSNP is a really flexible tool mapped paired data. You can give parameters on the config.yaml file to RattleSNP to generate a modular, dedicated pipeline for your own data.

Mapping 

RattleSNP includes (at the moment) only BWA tools.

Included tools :

BWA_MEM http://bio-bwa.sourceforge.net/bwa.shtml
BWA_SAMPE http://bio-bwa.sourceforge.net/bwa.shtml

Optional statistics 

Using RattleSNP you can activate or deactivate statistics on mapping steps.

Directed acyclic graphs (DAGs) show the differences between deactivated (BUILD_STATS=False):

and activated BUILD_STATS step on configuration file (BUILD_STATS=True):

Warning

In any case, MAPPING will be activated if BUILD_STATS is True even if MAPPING-ACTIVATE is False

SNP calling 

The SNP calling is perform by GATK tools.

Included tools :

GATK version >= 4.0.0 https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4

Filter VCF and genetics tools 

From fastq to bam

Mapping

Optional statistics

SNP calling

Filter VCF and genetics tools