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 (1.5-1.6Â 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 |