From: Best practices for variant calling in clinical sequencing
Strategy | Variant callers |
---|---|
Alignment and pre-processing | |
Read alignment | |
Marking duplicates | |
BAM file creation | |
Sequencing metrics | |
Sample quality control | |
Variant calling | |
Inherited SNVs/indels | FreeBayes [36], GATK HaplotypeCaller [19], Platypus [20], Samtools/BCFtools [37] |
Somatic mutations | deepSNV [38], MuSE [39], MuTect2 [40], SomaticSniper [41], Strelka2 [42], VarDict [43], VarScan2 [44] |
Copy number variants | cn.MOPS [45], CONTRA [46], CoNVEX [47], ExomeCNV [48], ExomeDepth [49], XHMM [50] |
Structural variants | DELLY [51], Lumpy [52], Manta [53], Pindel [54], SVMerge [55] |
Gene fusions (RNA-seq) | fusionCatcher [56], fusionMap [57], mapSplice [58], SOAPfuse [59], STAR-Fusion [60], TopHat-Fusion [61] |
Variant review/storage | |
Visualization and review | |
VCF/BCF file manipulation | BCFtools [37] |