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Reference Databases Needed
===================

To run the pipelines, you will need to have reference databases installed on your cluster. If you are using the
AWS installation, these databases are provided for you.  If you need to install your references, please install the ones below.
Omics Pipe is compatible with all species genome files.  Examples below are for hg19, but you can substitute them for the equivalent files from other species. 

All Pipelines
===========

Genome
------------------

* .fa file can be downloaded from: `<http://cufflinks.cbcb.umd.edu/igenomes.html>`_

Reference Annotation Files
------------------------------
You can use any reference annotations you would like, as long as they are GTF files. 

Examples include: 

* gencode.v18.annotation.gtf

* UCSC genes.gtf

References for Variants (RNA-seq cancer, RNA-seq cancer TCGA, WES and WGS pipelines)
==============

* dbsnp_137.hg19.vcf

* Mills_and_1000G_gold_standard.indels.hg19.vcf

* 1000G_phase1.indels.hg19.vcf

* hapmap_3.3.hg19.vcf

* 1000G_omni2.5.hg19.vcf

* dbNSFP2.0.txt

* common_no_known_medical_impact_00-latest.vcf

* cadd.tsv.gz

* drugbank.tsv

* cosmic.tsv

* clinvar.txt


WES Pipeline 
======

* truseq_exome_targeted_regions.hg19.bed


ChIP-seq Pipelines
========
* hg19.chrom.sizes


SNPiR Pipelines (RNA-seq cancer and RNA-seq cancer TCGA pipelines)
==============================================

* BWA Index

* RNA editing sites (Human_AG_all_hg19.bed)

* RepeatMasker.bed

* anno_combined_sorted