================================= Tools and software ================================= BALSAMIC ( **version** = 14.0.1 ) uses myriad of tools and softwares to analyze fastq files. This section covers why each one is included: usage and parameters, and relevant external links. ascatNgs ~~~~~~~~ :Source code: `GitHub` ``_ :Article: `PNAS` ``_ :Version: `4.5.0` bcftools ~~~~~~~~ :Source code: `GitHub` ``_ :Article: `Bioinformatics` ``_ :Version: `>=1.10` bedtools ~~~~~~~~ :Source code: `GitHub` ``_ :Article: `Bioinformatics` ``_ :Version: `2.30.0` bwa ~~~ :Source code: `GitHub` ``_ :Article: `Bioinformatics` ``_ :Version: `0.7.17` cadd ~~~~ :Source code: `GitHub` ``_ :Article: `Nature Genetics` ``_ :Version: `1.6` cnvkit ~~~~~~ :Source code: `GitHub` ``_ :Article: `PLOS Computational Biology` ``_ :Version: `0.9.9` cnvpytor ~~~~~~~~ :Source code: `GitHub` `` :Article: `GigaSciences` `` :Version: `1.3.1` delly ~~~~~ :Source code: `GitHub` ``_ :Article: `Bioinformatics` ``_ :Version: `1.0.3` ensembl-vep ~~~~~~~~~~~ :Source code: `GitHub` ``_ :Article: `Genome Biology` ``_ :Version: `104.3` fastp ~~~~~ :Source code: `GitHub` ``_ :Article: `Bioinformatics` ``_ :Version: `0.23.2` fastqc ~~~~~~ :Source code: `GitHub` ``_ :Article: `Babraham` ``_ :Version: `0.11.9` gatk ~~~~ :Source code: `Github` ``_ :Article: `Current Protocols in Bioinformatics` ``_ :Version: `3.8` genmod ~~~~~~ :Source code: `Github` ``_ :Version: `0.2.16` manta ~~~~~ :Source code: `GitHub` ``_ :Article: `Bioinformatics` ``_ :Version: `1.6.0` mosdepth ~~~~~~~~ :Source code: `GitHub` ``_ :Article: `Bioinformatics` ``_ :Version: `0.3.3` multiqc ~~~~~~~ :Source code: `GitHub` ``_ :Article: `Bioinformatics` ``_ :Version: `1.12` picard ~~~~~~ :Source code: `GitHub` ``_ :Article: `-` :Version: `2.27.1` sambamba ~~~~~~~~ :Source code: `GitHub` ``_ :Article: `Bioinformatics` ``_ :Version: `0.8.2` samtools ~~~~~~~~ :Source code: `GitHub` ``_ :Article: `Bioinformatics` ``_ :Version: `>1.11` sentieon-tools ~~~~~~~~~~~~~~ :Source code: `Commercial Tool` ``_ :Article: `Bioinformatics` ``_ :Version: `202010.02` somalier ~~~~~~~~ :Source code: `Github` ``_ :Article: `Genome Medicine` ``_ :Version: `0.2.16` svdb ~~~~ :Source code: `Github` ``_ :Article: `F1000Res` ``_ :Version: `2.8.1` tabix ~~~~~~ :Source code: `GitHub` ``_ :Article: `Bioinformatics` ``_ :Version: `>=1.11` tiddit ~~~~~~ :Source code: `Github` ``_ :Article: `F1000Res` ``_ :Version: `3.3.2` vardict ~~~~~~~ :Source code: `GitHub` ``_ :Article: `Nucleic Acid Research` ``_ :Version: `2019.06.04` vcfanno ~~~~~~~ :Source code: `GitHub` ``_ :Article: `Genome Biology` ``_ :Version: `0.3.3` vcf2cytosure ~~~~~~~~~~~~~ :Source code: `GitHub` ``_ :Article: `-` :Version: `0.8`