example

Examples with tiny unrealistic demo data after SomaticSeq is properly installed

Run SomaticSeq for tumor-normal mode

/PATH/TO/somaticseq/tests/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 your current directory. 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.

Run SomaticSeq for tumor-only mode

Similar to above

cd example
/PATH/TO/somaticseq/tests/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.

Run dockerized workflow with MuTect2, VarDict, and Strelka2 in tumor-normal mode

If you are able to run docker, you may test the following workflow:

cd example
/PATH/TO/somaticseq/tests/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.

dockerized workflow with tumor-only mode.

Same as above, but run the /PATH/TO/somaticseq/tests/example/invoke_dockerized_tumor_only_callers.sh.