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Revision as of 12:44, 23 October 2014
, 12:44, 23 October 2014→Human Reference Files
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In addition to the fasta file a few additional files are required.
* Already included with default reference files
* If you are using your own reference files, you will need to be sure to create these files
** Be sure to create these additional files using the version of tool being run by GotCloud (by default they are in the gotcloud/bin/ directory)
** In the commands below, replace ref.fa with the path/name of the reference fasta file
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! Step !! Required Extensions !! Command to Create
! Pipeline !! Step !! Required Extensions !! Command to Create !! More Information
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|all || -bs.umfa || automatically created in same directory as REF file by GotCloud
| all || ||.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
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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
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| align || qplot || .winsize100.gc || <code>bin/qplot --reference ref.fa || NOTE: Ignore the error at the end of qplot that says:
<pre>FATAL ERROR -
No SAM/BAM files provided, stopped!</pre>
This error is due to using qplot to just generate a GC Content file and not also process a BAM file.
[[QPLOT#Input_files|QPLOT: InputFiles]]
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=== DBSNP VCF File ===
=== DBSNP VCF File ===
