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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 http://download.bpipe.org/
vt 1.0 Vcf manipulation tool set http://genome.sph.umich.edu/wiki/Vt
Igvtools 2.3.72 IGV tools, used for indexing VCF files for use by IGV https://www.broadinstitute.org/igv
Fastqc 0.10.1 Fatsq file quality assessment tool http://www.bioinformatics.babraham.ac.uk/projects/fastqc
Samtools 0.1.18 BAM and other file manipulation tool https://sourceforge.net/projects/samtools
VarScan 2.3.3 Variant caller for SNPs and indels http://sourceforge.net/projects/varscan
Gatk 3.4 Genome analysis toolkit from Broad Institute https://software.broadinstitute.org/gatk
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 http://sourceforge.net/projects/picard
Ensembl DB 78 - 85 Annotation and consequences database http://www.ensembl.org
Bcl2fastq 2.17.1 Illumina BCL to fastq file convertor https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html
  1. The upstream amplicon pipeline has a number of external tool dependencies which are shown in this table