See http://genome.sph.umich.edu/wiki/GotCloud for full GotCloud documentation.
Before running GotCloud, you need to compile the source:
cd src/; make; cd ..
To test GotCloud, run:
gotcloud test
Results are self-checked. If errors occur, the output will say so. If all tests complete successfully, the output will be deleted.
The output directory will be listed near the top of the output.
To preserve the output files for inspection even when gotcloud runs without errors, run:
gotcloud test --leave-a-mess
Variant Calling requires three types of input files:
a set of BAM files
index file
Each line contains at least 3 space-separated columns representing a single individual:
[SAMPLE_ID] [COMMA SEPARATED POPULATION LABELS] [BAM_FILE1] [BAM_FILE2] ...
1 or more BAMs are allowed per individual
configuration file
Contains run-time options & command line arguments.
A default configuration is provided.
User must specify:
BAM_INDEX =
# the path/name of the index fileOUT_DIR
Optional specifications...
CHRS =
#space separated list of chromosomes - defaults to 1-22 & XRefer to the default configuration & the wiki page for more information on other settings.
Optional input files:
Once these files are configured, to run snp calling and process the data:
{path}gotcloud snpcall --conf {conf_file} \
--outdir {output_directory} --numjobs {# of threads to use for processing}