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Revision as of 10:35, 23 October 2014
, 10:35, 23 October 2014→Reference Files
*** Use <code>bin/bwa index ref.fa</code> if you need to generate the bwa reference files (.amb, .ann, .bwt, .pac, .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: REF - specify the ref.fa/ref.fa.gz name
** Configuration Name: REF - specify the ref.fa/ref.fa.gz name
* DBSNP File
* DBSNP File - used for recalibration & qplot
** VCF file containing dbsnp variants
** VCF file containing dbsnp variants
** Configuration Name: DBSNP_VCF
** Configuration Name: DBSNP_VCF
* HapMap3 VCF
* HapMap3 VCF - used for VerifyBamID
** VCF file containing HM3 variants
** VCF file containing HM3 variants
** Configuration Name: HM3_VCF
** Configuration Name: HM3_VCF
