README

Oncotator requires Python 2.7 and the following python libraries installed

pyvcf
pysam
biopython

Samtools and Tabix are required if you want to create indexed vcf files for use with Oncotator.

### example GAF and dbSNP index commands are below

wget https://tcga-data.nci.nih.gov/docs/GAF/GAF3.0/transcript.genome.v3_0.gaf.gz
gunzip transcript.genome.v3_0.gaf.gz
oncotator-index.py gaf transcript.genome.v3_0.gaf

wget https://tcga-data.nci.nih.gov/docs/GAF/GAF3.0/UCSCgene.Jan2012.v3_0.fa.gz
gunzip UCSCgene.Jan2012.v3_0.fa.gz
oncotator-index.py gaf-seqs UCSCgene.Jan2012.v3_0.fa

## For dbSNP annotations
wget ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz
wget ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz.tbi

## OR

bgzip dbsnp_build_135.vcf
tabix -p vcf dbsnp_build_135.vcf.gz

## For Cosmic annotations
wget ftp://ftp.sanger.ac.uk/pub/CGP/cosmic/data_export/CosmicMutantExportIncFus_v62_291112.tsv.gz
gunzip CosmicMutantExportIncFus_v62_291112.tsv.gz
oncotator-index.py cosmic CosmicMutantExportIncFus_v62_291112.tsv