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 |