cd example
./paired_somaticseq_example.sh
This example uses the outputs from MuTect2, VarDict, and Strelka2 as input. This
is just an example. There are additional callers that are officially supported
besides those three. If this command is run successfully, the directory
paired_somaticseq
will be created. In it, SomaticSeq TSV files, VCF files, and
ada classifiers will be created. Do not use those classifiers for anything
other than demo purposes. They are for demo purposes and completely useless.
Similar to above
cd example
./single_somaticseq_example.sh
The directory will be single_somaticseq
.
To check the results of paired_somaticseq_example.sh
and/or single_somaticseq_example.sh
, run results_check.sh
.
If you are able to run docker, you may test the following workflow:
cd example
./invoke_dockerized_tumor_normal_callers.sh
Then, the following scripts will be created and executed:
paired_example/{1,2}/logs/mutect2.year.month.date.timestamp.cmd
paired_example/{1,2}/logs/strelka.year.month.date.timestamp.cmd
paired_example/{1,2}/logs/vardict.year.month.date.timestamp.cmd
paired_example/{1,2}/SomaticSeq/logs/somaticSeq.year.month.date.timestamp.cmd
paired_example/logs/mergeResults.year.month.date.timestamp.cmd
Directories 1 and 2 are created because the script invokes two parallel
processes using -nt 2
. The caller scripts (i.e., mutect2, strelka, and
vardict) will be executed first by two parallel processes (-nt 2
). Then, the
somaticSeq scripts will be executed. Finally, the mergeResults script will be
executed.
Same as above, but run the invoke_dockerized_tumor_only_callers.sh
.