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Table 1 Best practices for optimal identification of indels in human next-generation sequencing data

From: Comparison of insertion/deletion calling algorithms on human next-generation sequencing data

Target Small (1–10 bp) indels Mid-sized (10–100 bp) indels Large (>2000 bp) deletions**
Human 200 gene TES capture (1.5-1.6 Mb) with read depth ~600x GATK-HC Run both GATK-HC and Pindel with adjustments to parameters*. Pindel
Validate with Pindel helpful if analyzing <6 samples
Human WES capture (65–75 Mb) with read depth ~100x GATK-HC Run both GATK-HC and Pindel with adjustments to parameters*. Pindel
Validate with Pindel helpful if analyzing <6 samples
Human WGS capture (3.2 Mb) with read depth ~30x GATK-HC Run both GATK-HC and Pindel with M = 3. Pindel
Validation with Pindel may be helpful, but run with M = 3
  1. *Adjust Pindel M value to 10 if analyzing single sample; adjust M to 30 if analyzing multiple samples.
  2. **Pindel does not identify large insertions, but can identify the breakpoints for these insertions. These were not included in this analysis.