A pipeline for distributed SNP calling
- Scala
- sbt
- Picard library (I have a separate script which fetches it automatically (
download_picard.sh
), but if not, placesam-<version>.jar
andpicard-<version>.jar
in lib/)
In the root directory:
sbt package
This compiles and puts a biggie.jar file in build/. If you just want to compile without packaging, run:
sbt compile
./bin/biggie cmd args ...
Commands
all alignment.bam reference.fa
classify sorted-BAM-file
snp alignment.bam reference.fa regions.txt
regions.txt: refSeq start end
e.g. chr21 14800232 14804369