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Table 2 Pipeline dependencies

From: PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories

Tool Version Description Link
Bpipe 0.9.8 Pipeline workflow framework
vt 1.0 Vcf manipulation tool set
Igvtools 2.3.72 IGV tools, used for indexing VCF files for use by IGV
Fastqc 0.10.1 Fatsq file quality assessment tool
Samtools 0.1.18 BAM and other file manipulation tool
VarScan 2.3.3 Variant caller for SNPs and indels
Gatk 3.4 Genome analysis toolkit from Broad Institute
Primal aligner 1.01 In-house developed amplicon aligner in Perl  
Canary 0.9 In-house developed amplicon aligner and variant caller in Java Manuscript in preparation
NormaliseVcf 1.2 In-house VCF normalisation tool for annotating VCFs with gene, transcript and HGVS nomenclature Manuscript in preparation
Picard 1.141 Tools for manipulating high-throughput sequencing (HTS) data
Ensembl DB 78 - 85 Annotation and consequences database
Bcl2fastq 2.17.1 Illumina BCL to fastq file convertor
  1. The upstream amplicon pipeline has a number of external tool dependencies which are shown in this table