|
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
|
