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 |