GotCloud: Variant Calling Pipeline: Difference between revisions
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Terry Gliedt (talk | contribs) Created page with 'Back to the beginning [http://genome.sph.umich.edu/wiki/Pipelines] Running umake is straightforward: <code> '''cd ~/myseq''' '''/usr/local/biopipe/bin/umake --conf myconf ???…' |
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Back to the beginning [http://genome.sph.umich.edu/wiki/Pipelines] | Back to the beginning [http://genome.sph.umich.edu/wiki/Pipelines] | ||
The Variant Calling Pipeline (UMAKE) takes recalibrated BAM files and detects SNPs and calls their genotypes, producing VCF files. | |||
== Input Data:== | |||
*Aligned/Processed/Recalibrated BAM files | |||
*Index file containing Sample IDs & BAM file names | |||
*Reference files | |||
*(Optional) Configuration file to override default options | |||
=== BAM files === | |||
=== Index file === | |||
=== Reference Files === | |||
=== Configuration File === | |||
== Running == | |||
Running umake is straightforward: | Running umake is straightforward: | ||
Revision as of 17:49, 5 November 2012
Back to the beginning [1]
The Variant Calling Pipeline (UMAKE) takes recalibrated BAM files and detects SNPs and calls their genotypes, producing VCF files.
Input Data:
- Aligned/Processed/Recalibrated BAM files
- Index file containing Sample IDs & BAM file names
- Reference files
- (Optional) Configuration file to override default options
BAM files
Index file
Reference Files
Configuration File
Running
Running umake is straightforward:
cd ~/myseq
/usr/local/biopipe/bin/umake --conf myconf ???
make -f [out-prefix].Makefile -j [# parallel jobs]
