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Jump to navigationJump to searchTutorial: EMMAX GotCloud STOM: Lecture 6 (view source)
Revision as of 09:58, 6 January 2014
, 09:58, 6 January 2014→Preparing Input Files
* Configuration File - See the example configuration file below.
* Configuration File - See the example configuration file below.
cat $S5/examples/index/chr7.CFTR.low_coverage.conf
CHRS = 7
CHRS = 7
(WARNING: This step will take a long time, up to 5 minutes, because it processes nearly 100 BAMs, 4 jobs simultaneously at a time)
(WARNING: This step will take a long time, up to 5 minutes, because it processes nearly 100 BAMs, 4 jobs simultaneously at a time)
time $S5/gotcloud/gotcloud snpcall --conf � $S5/examples/index/chr7.CFTR.low_coverage.conf � --outDir ~/out/snps --baseprefix $S5/examples � --region 7:117000000-117500000 --numjobs 4
time $S5/gotcloud/gotcloud snpcall --conf $S5/examples/index/chr7.CFTR.low_coverage.conf --outDir ~/out/snps --baseprefix $S5/examples --region 7:117000000-117500000 --numjobs 4
* Check the summary statistics of SNP call to evaluate its quality
* Check the summary statistics of SNP call to evaluate its quality
(WARNING: This step will take a long time, up to 2 minutes)
(WARNING: This step will take a long time, up to 2 minutes)
time $S5/gotcloud/gotcloud beagle --conf � $S5/examples/index/chr7.CFTR.low_coverage.conf � --outDir ~/out/snps --baseprefix $S5/examples � --region 7:117000000-117500000 --numjobs 2
time $S5/gotcloud/gotcloud beagle --conf $S5/examples/index/chr7.CFTR.low_coverage.conf --outDir ~/out/snps --baseprefix $S5/examples --region 7:117000000-117500000 --numjobs 2
=== Understanding the Output Files ===
=== Understanding the Output Files ===
