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Revision as of 18:15, 6 November 2012
, 18:15, 6 November 2012no edit summary
* Write loci file when performing pileup
* Write loci file when performing pileup
** WRITE_TARGET_LOCI = TRUE
** WRITE_TARGET_LOCI = TRUE
* Specify the directory to store target information, for example: targetDir
* Specify the output sub-directory to store target information, for example: targetDir
** Should not be a full path as this will co under the OUTDIR directory.
** TARGET_DIR = targetDir
** TARGET_DIR = targetDir
== Running on a Cluster ==
=== Running on a Cluster ===
To run on the Cluster, the following settings need to be added to the configuration file:
To run on the Cluster, the following settings need to be added to the configuration file:
MOS_PREFIX = mosrun -E/tmp -t -i
MOS_PREFIX = mosrun -E/tmp -t -i
=== Results ===
If there is a failure, you should see a message like:
make: *** [...] Error 1
Where ... is filled in with other text indicating what step failed.
On SNP Call success, you should see the following output sub-directories under your output directory:
* glfs with a bams & samples subdirectory
* pvcfs with a subdirectory per chromosome and then per region
* split with a subdirectory per chromosome
* vcfs with a subdirectory per chromosome
* (optionally your target directory)
Under the vcf/chrXX directory, there should be:
* chrXX.filtered.sites.vcf
* chrXX.filtered.sites.vcf.log
* chrXX.filtered.sites.vcf.summary
* chrXX.filtered.vcf.gz
* chrXX.filtered.vcf.gz.OK
* chrXX.filtered.vcf.gz.tbi
* chrXX.merged.sites.vcf
* chrXX.merged.stats.vcf
* chrXX.merged.vcf
* chrXX.merged.vcf.OK
Under the split/chrXX directory, there should be:
* chrXX.filtered.PASS.split.[N].vcf.gz
* chr20.filtered.PASS.split.err
* chr20.filtered.PASS.split.vcflist
* chr20.filtered.PASS.gz
* subset.OK
