Table 2.
Pipeline dependencies
| 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 |
The upstream amplicon pipeline has a number of external tool dependencies which are shown in this table