Changes

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, .GCContent, .amb, .ann, .bwt, .pac, .rbwt, .rpac, .rsa, .sa  

** Files required: .fa, -bs.umfa, .GCContent, .amb, .ann, .bwt, .pac, .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.  

*** 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>  

*** .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, .sa)  

** Configuration Name: FA_REF - specify the ref.fa/ref.fa.gz name  

** Configuration Name: REF - specify the ref.fa/ref.fa.gz name  

* DBSNP File  

* DBSNP File  

** tab delimited file/VCF, can be compressed

** VCF file containing dbsnp variants

** Configuration Name: DBSNP_VCF  

** Configuration Name: DBSNP_VCF  

* PLINK-compatible binary genotype files

* HapMap3 VCF

** Files required: .bed, .bin, .fam

** VCF file containing HM3 variants

** Configuration Name: PLINK

** Configuration Name: HM3_VCF

=== Configuration File ===  

=== Configuration File ===