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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:

File (Directory) Name Description
ReadQC/ Statistical summaries for QC (e.g., histogram of depth distribution)
Param/ Parameter information
Data/ Temporary data used by cisMuton internally
Call.${BG_SAMPLE_NAME}/ Main output directory

Call.${BG_SAMPLE_NAME} contains the following files:

File (Directory) Name Description
info.filter/ Table showing how each filter worked for call candidates
call.case0.txt Call table
call.case0.txt.vcf Call table (vcf format)

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

2.2. Output Format of the Call Table

Column Description
Chr Chromosome name
Start Start position (1-based)
End End position (1-based)
Reference Reference nucleotide
Variant Variant nucleotide
FPscore -log10 P value in Fisher's exact test
VFreqRatio Ratio of VAF in tumor to VAF in the normal case
VariantFreq VAF, variant allele frequency
DelPivotPos Position used as the pivot of deletion of deletion
Insertion Insertion sequence
Depth:FG Depth at this position in the foreground (described as ${SAMPLE_NAME} above)
Depth:BG Depth at this position in the background (described as ${BG_SAMPLE_NAME} above)
A,C,G,T,D,I:FG Nucleotide counts at this position in the foreground
A,C,G,T,D,I:BG Nucleotide counts at this position in the background
Homopolymer:Length Length of homopolymer surrounding the variant position
CopyNumber:Ratio Ratio of normalized depth in the tumor sample to the normal sample at this position. The depth is normalized by the average in each sample.
Variant SNP:MajorAlleleFreq VAF of most frequently observed variant
DBSnp DBsnp annotation
JPSnp JPsnp annotation
... (Annotations continue in this and successive columns)
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