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Fig. 1 | BMC Bioinformatics

Fig. 1

From: Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers

Fig. 1

Workflow of the comparison of the nine variant callers. A heterogeneous cancer sample is simulated based on a real renal cell carcinoma sample (steps 1, 2 and 3). Two different alignment settings and eight different coverage and normal contamination levels are employed (steps 4 and 5). The variant callers deepSNV, GATK HP, GATK UG, JointSNVMix2, MuTect, SAMtools, SiNVICT, somaticSniper and VarScan2 are run on all bam files (step 6). The performance of the different tools is evaluated and analyzed in detail (step 7). The tools are also assessed when using various pipeline or parameter modifications as described in Section “Pipeline and parameter improvements”. A more detailed description of the pipeline and the evaluation procedure can be found in the Methods Section as well as in Additional file 1: Section B, and Additional file 1: Section C

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BMC Bioinformatics

ISSN: 1471-2105

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