SNPs across 15 populations of H.glycines

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Organism: 
Heterodera glycines v2 (Soybean Cyst Nematode (v2))
Program, Pipeline Name or Method Name: 
GATK Best Practices: BWA-mem, Picard, GATK
Program, Pipeline or Method version: 
BWA 0.7.13, Picard 2.4.1, GATK 3.5
Source Name: 
SNPs called from 15 populations of H. glycines
Time Executed: 
04/06/2018
Materials & Methods (Description and/or Program Settings): 
SNPS from fifteen H. glycines populations (TN22, TN8, TN7, TN15, TN1, TN21, TN19, LY1, OP50, OP20, OP25, TN16, PA3, G3). Reads were aligned with BWA-MEM. BAM files were sorted, cleaned, marked for duplicates, read groups were added with Picard. SNP/Indel realignment were performed prior to calling SNPs and Indels with GATK.