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Revision as of 14:04, 23 October 2014
, 14:04, 23 October 2014→Reference Files
=== Reference Files ===
=== Reference Files ===
See [[GotCloud: Genetic Reference and Resource Files]] for detailed information about the multiple required reference files for the alignment pipeline, including:
* How to obtain default references
* Configuration keys & default values
* How to generate your own references
* How to point GotCloud to your reference files
Required Reference File Types:
* [[GotCloud: Genetic Reference and Resource Files#Reference fasta Files|Reference fasta Files]]
* [[GotCloud: Genetic Reference and Resource Files#DBSNP VCF Files|DBSNP VCF Files]]
*** If you don't have the -bs.umfa file, the software will try to create it in the same directory as the reference fasta.
* [[GotCloud: Genetic Reference and Resource Files#HapMap3 VCF Files|HapMap3 VCF Files]]
*** Use <code>bin/bwa index ref.fa</code> if you need to generate the bwa reference files (.amb, .ann, .bwt, .pac, .sa)
** VCF file containing HM3 variants
=== Configuration File ===
=== Configuration File ===
