The_Other_WPT_Study

Pipeline

SNPs and indels were called according to the GATK best practices pipeline for RNA-seq

If you have the all of the software (with correct versions) downloaded, you can run the command below to download the data and generate SNPs and indels.

bash Pipeline_Commands.sh

Note:

• The scripts that are called use multple threads, please make sure to check that your machine has enough threads, or modify the scripts accordingly.
• You will also need to download/index the soy a2.v1 genome and modify STAR_Commands.txt to point to your .fa and .gff file locations (see STAR_index.sh for an example)

Versions of software used

lftp 4.38.1
GNU parallel 20160822
FastQC 0.11.5
Cutadapt 1.8.1
STAR 2.5.3a
Picard Tools 2.9.2
GenomeAnalysisTK 3.7-0
VCFtools 0.1.15
BEDtools 2.25.0