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OUT_PREFIX = {output_prefix}
OUT_PREFIX = {output_prefix}
where {output_prefix} is the name of the folder in which you want the output to be stored.
where {output_prefix} is a prefix to the name of the Makefiles that will be generated by UMAKE.
An additional option can be added in the configuration file:
OUT_DIR = {OUT_DIR}
where {OUT_DIR} is the name of directory in which you want the output to be stored. If you do not specify this in the configuration file, you will need to add an extra parameter when you run UMAKE in the next step.
===Running UMAKE===
If you added an OUTDIR line to the configuration file, you can run UMAKE with the following command:
{ROOT_DIR}/bin/umake.pl --conf umake_test.conf --snpcall --numjobs 2
If you have not added an OUTDIR line to the configuration file, you can specify the output directory directly with the following command:
{ROOT_DIR}/bin/umake.pl --conf umake_test.conf --outdir {OUT_DIR} --snpcall --numjobs 2
where {OUT_DIR} is the directory in which you want the output to be stored.
Either command will perform SNP calling on the test samples. The resulting VCF files from this will be located in {OUT_DIR}/vcfs/chr20.
==Advanced Options==
For further explanation about the other options available in the alignment pipeline, see the [[Mapping_Pipeline|Mapping Pipeline]] page.
For further explanation about the other options available in UMAKE, see the [[Variant_Calling_Pipeline_(UMAKE)|Variant Calling Pipeline]] page.
