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Revision as of 14:04, 23 October 2014
, 14:04, 23 October 2014→Additional files generated from the reference fasta
! Pipeline !! Step !! Required Extensions !! Command to Create !! More Information
! Pipeline !! Step !! Required Extensions !! Command to Create !! More Information
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|-
| all || ||.fai || <code>bin/samtools faidx ref.fa</code>
| align, snpcall, indel || ||.fai || <code>bin/samtools faidx ref.fa</code>
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|-
| all || || -bs.umfa || automatically created in same directory as REF file by GotCloud
| align, snpcall, indel || || -bs.umfa || || If it does not already exist, GotCloud automatically creates this file in same directory as the REF file
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|-
| align || bwa mapping || .amb, .ann, .bwt, .pac, .sa || <code>bin/bwa index ref.fa</code> || http://bio-bwa.sourceforge.net/bwa.shtml
| align || bwa mapping || .amb, .ann, .bwt, .pac, .sa || <code>bin/bwa index ref.fa</code> || http://bio-bwa.sourceforge.net/bwa.shtml
