Heterodera glycines TN10DraftAssembly

SNPs across 15 populations of H.glycines

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

April 6, 2018, midnight

Category

Molecular markers (QTL)

Description

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.

File

sortedrenamed.combined_variants.vcf.gz

Index

sortedrenamed.combined_variants.vcf.gz.tbi