Set of variant callers integrated

[szilvajuhos]

List of somatic callers at https://omictools.com/somatic-snp-detection-category

• [x] MuTect2: ready
• [x] Strelka: very cumbersome to use https://sites.google.com/site/strelkasomaticvariantcaller/
• [x] VarDict/VarDictJava : https://github.com/AstraZeneca-NGS/VarDictJava: cumbersome
• [x] Bambino: vaporware
• [x] Bassovac: vaporware
• [x] Cake: vw
• [ ] CLImAT: http://bioinformatics.ustc.edu.cn/CLImAT/
• [ ] DeNovoGear: https://github.com/denovogear/denovogear
• [ ] EBCall: https://github.com/friend1ws/EBCall
• [x] FasD-Somatic: SNPs only
• [x] Hapmuc: vw
• [x] JointSNVMix: vw
• [ ] LocHap: http://www.compgenome.org/lochap/
• [x] LoLoPicker: alpha
• [x] MSIsensor: microsatellites only
• [x] MultiSNV: SNVs only
• [x] mutationSeq: vw
• [x] Polymutt: vw
• [ ] qSNP/AdamaJava: https://sourceforge.net/projects/adamajava/
• [x] qadgt: vw
• [x] RaReVator: vw
• [x] Radio: vw
• [x] RVD2: no
• [ ] samtools
• [x] Shimmer: vw
• [x] SNV-PPILP: vw
• [x] SNVMix: vw
• [x] SOAP: vw
• [x] SomaticCall: deprecated by MuTect2
• [ ] SomaticSeq: https://github.com/bioinform/somaticseq: worth to consider
• [x] SomaticSniper: https://github.com/genome/somatic-sniper. Looks like being dead
• [x] SomVarIUS: https://github.com/kylessmith/SomVarIUS For unpaired data
• [x] VariantMaster: vw
• [ ] VarScan: http://dkoboldt.github.io/varscan/
• [x] Virmid: vw
• [ ] DiscoSNP: https://gatb.inria.fr/software/discosnp/
• [ ] TakeABreak: https://gatb.inria.fr/software/takeabreak/
• [ ] MindTheGap: https://gatb.inria.fr/software/mind-the-gap/

[szilvajuhos]

What we have and going to integrate so far:

• [x] MuTect2
• [x] VarDict (only on milou)
• [x] MuTect1
• [x] Strelka (only on milou)
• [ ] samtools
• [ ] FreeBayes

[szilvajuhos]

The tiny dataset where we are expecting reads to be mapped is located at: chr1:130,738-143,733