How to get variation?
Pipeline of snp calling

1. We trimmed the adapter and filtered all low quality reads

2. We used the BWA (version: 0.6.2-r126) to map clean read to sorghum reference sequence (V2.1)

3. We used the SAMtools package to convert mapping results to BAM format

4. We used Picard(version: 1.87) program to eliminate duplicated reads generated during the process of library construction

5. We called the SNPs by the GATK (version: 2.5-2-gf57256b ) toolkit. We identified a set of SNPs based on the quality estimation scores generated by GATK (quality value >=30 and depth of coverage >=5)

6. We used the SnpEff program to annotate the SNPs including their genomic locations and coding effects.

Data Source
Reference sequences used in the process of snp calling.
Assembly Species Data type Version Source
Sorghum bicolar V2.1 BTx623 Genome data V2.1 http://www.phytozome.net
Sorghum bicolar V2.1 BTx623 Genome annotation V2.1 http://www.phytozome.net