cisMuton

cisMuton is a caller that detects SNVs/indels by comparing target (foreground) and control (background) samples.

cisMuton calls mutations from target capture regions, which are defined by the overlapping regions of ${GROUP}.target.bed and ${GROUP}.gene.bed.

Please read the Quick Start Guide for cisCall first for an outline of how to run cisMuton.

1. Running cisMuton

1.1. Basic Steps

The basic steps for running cisMuton are as follows.

1. Prepare all prerequisite files under the execution directory and set the parameters.
   For these inputs, see the Inputs and cisCall Installation section for further details.

2. Run cisMuton in the execution directory.

    $ cd /path_to_execute/
    $ perl /path_to_cisMuton_install_directory/qc_run.pl ${SAMPLE_NAME}:${BG_SAMPLE_NAME}:${GROUP}:MUTON,${OPTION}
   						

1.2. Removing Duplicates

The value for ${OPTION} can be set to remove PCR duplicates. This is strongly recommended for FFPE samples. See the Miscellaneous Options section to remove duplicates using cisCall.

1.3. Removing Adapter Sequences

Removing adapter sequences using cisCall must be done beforehand. See the Miscellaneous Options section for details.

2. cisMuton Outputs

Running cisMuton will create the following directories and a log file in the execution directory:

• output/: outputs
• tmp/: temporary files
• log.txt: log file

The following important points apply to files created inside tmp/:

• In the case of running cisMuton in the same execution directory after a preceding run, remove the tmp directory beforehand. Semaphore lock files with .lock cause abnormal program termination.
• The following .bam files will be used by cisCton:
  • ${SAMPLE_NAME}.${GROUP}.MUTON.TARGET/common.fastq.aln.bam
  • ${BG_SAMPLE_NAME}.${GROUP}.MUTON.TARGET/common.fastq.aln.bam
• In the case of FFPE samples, .bam file names generated by cisMuton may be slightly different, such as common.fastq.aln.none.bam.dup1331.bam and common.fastq.aln.bam.dup1110.bam, depending on the settings of cisMuton.

cisMuton first lists all possible variants with loose criteria and then applies filters to those found. It outputs intermediate files during these processes.

You can see examples of the output files (https://bioinfoncc-my.sharepoint.com/personal/bioinfo_bioinfoncc_onmicrosoft_com/_layouts/15/guestaccess.aspx?docid=0c67a92d4d78b4aaa9607050b0c199ae7&authkey=AXI4ilfH_ewBPSZ7YspHBhE) generated by cisMuton for the short example of test data.

2.1. Contents of the output/ Directory

Running cisMuton creates output/${SAMPLE_NAME}.${GROUP}/Muton/, which includes the following files:

Call.${BG_SAMPLE_NAME} contains the following files:

The file names of call tables may be slightly different depending on the settings of cisMuton.

2.2. Output Format of the Call Table