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Revision as of 23:49, 5 November 2012
, 23:49, 5 November 2012no edit summary
The following Reference Files are required:
The following Reference Files are required:
* Reference File fasta files
* Reference File fasta files
** Files required: .fa, -bs.umfa, .amb, .ann, .bwt, .pac, .rbwt, .rpac, .rsa, .sa
** Files required: .fa, -bs.umfa, .GCContent, .amb, .ann, .bwt, .pac, .rbwt, .rpac, .rsa, .sa
*** If you don't have the -bs.umfa file, the software will try to create it in the same directory as the reference fasta.
*** .GCContent can be generated using qplot, see: [[QPLOT#Input_files| QPLOT: Input Files: --gccontent]] and name the resulting file as <code>.fa.GCcontent</code>
*** Use <code>bin/bwa index ref.fa</code> if you need to generate the bwa reference files (.amb, .ann, .bwt, .pac, .rbwt, .rpac, .rsa, .sa)
*** Use <code>bin/bwa index ref.fa</code> if you need to generate the bwa reference files (.amb, .ann, .bwt, .pac, .rbwt, .rpac, .rsa, .sa)
** Configuration Name: FA_REF - specify the ref.fa/ref.fa.gz name
** Configuration Name: FA_REF - specify the ref.fa/ref.fa.gz name
*
* DBSNP File
** tab delimited file/VCF, can be compressed
*** 1st column -> chromosome
*** 2nd column -> 1-based position
** Configuration Name: DBSNP_VCF
** Configuration Name: DBSNP_VCF
*
* PLINK-compatible binary genotype files
** Files required: .bed, .bin, .fam
** Configuration Name: PLINK
** Configuration Name: PLINK
