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 | Â |
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 | https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html |