#!/bin/bash

toGATKformat.py /data/unsafe/autism/genomes/hg19/geneModels_Sep2013/refGene.txt.gz refGene-201309 
toGATKformat.py /data/unsafe/autism/genomes/hg19/geneModels_Sep2013/knownGene.txt.gz knownGene-201309
toGATKformat.py /data/unsafe/autism/genomes/hg19/geneModels_Sep2013/ccdsGene.txt.gz ccds-201309

joinGeneModels.py --g1=/data/unsafe/autism/genomes/hg19/geneModels_Sep2013/mitomap.txt --g2=refGene-201309.gz --output refGeneMito-201309