A simple distributed variant caller built using Apache Spark and ADAM.
variant-caller.sh <path to reference> <path to alignment> <output path> [options]
| Name | Description |
|---|---|
| -homozygousThreshold | Sets the homozygous threshold |
| -heterozygousThreshold | Sets the heterozygous threshold |
| -mapq | Filters reads based on the given mapq value |
| -debug | Turns on debug logging |