Contents of the output/ Directory

Running cisMuton creates output/<SAMPLE_NAME>.<PANEL>/ under the working directory, which includes the following directories:

Directory Name Description
Muton/ cisMuton output
Param/ Parameter information
Session/ Session information
ReadQC/ Statistical summaries for Read QC (e.g., histogram of depth distribution)
Report/ Report
Data/ Temporary data used by cisMuton internally

Muton/ contains the following directories:

Directory Name Description
Call.<BG_SAMPLE_NAME>/ Main output directory
CallQC/ QC for caller

Call.<BG_SAMPLE_NAME>/ contains the following files:

File Name Description
call.case0_WGENOME_dup.vcf * VCF file for called variants (main results)
call.case0_WGENOME_dup.txt * TSV file for filtered variants
  • * File names may be slightly different depending on the options of cisCall.

Output Format of the Call Table (VCF file)

  • The VCF file is based on VCF format 4.0.
  • Example values in the downloadable example output files may be sometimes odd due to the artificiality of the example input files.
  • Columns to be explained:

    Column Description
    ID ID appears only when a call matches with SNP ID.
    QUAL -log10 (p value) of Fisher’s exact test
    FILTER Please use calls with PASS. Filter names are shown when calls do not pass.

INFO Column

ID Description
AF VAF, variant allele frequency
DP Depth at this position in the foreground (tumor) data set
VFR Odds ratio from Fisher’s exact test (WILL BE UPDATED TO: ratio of VAF in the foreground to VAF in the background)
DPP Position used as the pivot of deletion
DPB Depth at this position in the background (normal) data set
FG Nucleotide counts at this position in the foreground for \|A\|C\|G\|T\|D\|I\|. D = deletion, I = insertion.
BG Nucleotide counts at this position in the background for \|A\|C\|G\|T\|D\|I\|. D = deletion, I = insertion.
HL Length of homopolymer surrounding this position.
SMAF VAF of most frequently observed variant.

The Last Column

ID Description
GT MEANINGLESS. Genotype.
DP Depth at this position in the foreground.
CN NOT USEFUL. Depth in the foreground / Depth in the background.
  • The tsv file in the same directory has (almost) the same contents but the format may be more useful in some cases.