richardxia / biggie

A pipeline for distributed SNP calling

BIGGIE: Big Genomics Inference Engine

A pipeline for distributed SNP calling

Requirements

• Scala
• sbt

Dependencies

• Picard library (I have a separate script which fetches it automatically (download_picard.sh), but if not, place sam-<version>.jar and picard-<version>.jar in lib/)

Compiling

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

Running

./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