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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