Contents of the output/ Directory
Running cisMuton creates output/<SAMPLE_NAME>/ 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 |
Report/ |
Report |
Muton/ contains the following files and a directory:
| File Name |
Description |
muton_wgenome.vcf |
VCF file for called variants |
<SAMPLE_NAME>.ciscall.mem.bam |
BAM file |
<SAMPLE_NAME>.ciscall.mem.bam.bai |
BAM index file |
Data/ |
Temporary data used by cisMuton |
- 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. |
VOR |
Variant Odds Ratio. |
FPV |
Fisher p-value. |
FQV |
Fisher q-value. |
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. |