Difference between revisions of "GotCloud: Variant Calling Pipeline"
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Jump to navigationJump to searchTerry 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] | ||
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| + | 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]
