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Table 2 The PGen workflow consists of several individual tasks with diverse core and memory requirements, which were assigned based on tools’ applicability of multiple threads and memory cost after testing

From: PGen: large-scale genomic variations analysis workflow and browser in SoyKB

Tasks Base code Cores (Threads) Memory (GB)
Indexing of reference genome BWA/samtools/picard tools 1 4
Alignment to reference genome BWA 1 21
Sorting sam files Picard tools 1 21
Removal of PCR duplicates Picard tools 1 21
Add or replace read groups Picard tools 1 21
Create realign target GATK_RealignerTargetCreator 15 20
Realign indels GATK_IndelRealigner 1 10
Calling variants GATK_HaplotypeCaller 1 3
Select SNPs and indels GATK_SelectVariants 14 10
Filtering variants GATK_VariantFiltration 14 10
Create genotype GVCF GATK_GenotypeGVCFs 1 10
Merge GVCFs GATK_CombineGVCFs 1 20
Combine variants GATK_CombineVariants 1 10
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