GATK Best Practices: BWA-mem, Picard, GATK
BWA 0.7.13, Picard 2.4.1, GATK 3.5
SNPs called from 15 populations of H. glycines
April 6, 2018, midnight
Molecular markers (QTL)
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.
sortedrenamed.combined_variants.vcf.gz