Contents of the output/ Directory
Running cisFusion creates output/<SAMPLE_NAME>/ under the working directory, which includes the following directories:
| Directory Name |
Description |
Cton/ |
cisCton output |
Param/ |
Parameter information |
Cton/ contains the following files and a directory:
| File (Directory) Name |
Description |
gene.cnv_wgenome.vcf |
Call table for genes (VCF format) |
gene.cnv_wgenome.txt |
Call table for genes (TSV format) |
seg.cnv_wgenome.vcf |
Call table for target bed regions (VCF format) |
bed.cnv_wgenome.txt |
Call table for target bed regions (TSV format) |
<SAMPLE_NAME>_wgenome_dup.exonlrr.pdf |
Log R ratio graph of exon regions |
supplement/ |
Other supplementary information |
(1) Call Table for CNA Segments
- 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.
- In VCF (seg…vcf), one line represents one segment, which is composed of points each of which represents a targeted bed region with a logR value. In TSV (bed…txt), one line represents such a point, where multiple lines with the same Segment.Id belong to the same segment.
-
Columns to be explained:
| Column |
Description |
ID |
MEANINGLESS |
QUAL |
MEGNINGLESS |
FILTER |
Please use calls with PASS. |
INFO Column
| ID |
Description |
SVTYPE |
Type of structural variant (CNV). |
END |
End position of the segment |
SVLEN |
Length of the segment |
PV |
p-value for segment calling (bootstrapping test) |
ES |
Effect size for segment calling (median logR in the real data –median logR in the randomized data) |
MLR |
Median log R of the bed regions of the segment |
ORGSEG |
Original segment ID before splitting segments by low resolution regions |
ORGABN |
Normal segment (=F) or reevaluated bed as a segment in an abnormal segment (=T) |
GENE |
Genes overlapping with the bed regions |
LR |
Log2 ratios of the bed regions |
CDF |
GC-corrected depths of the bed regions in the foreground (tumor) data set |
CDB |
GC-corrected depths of the bed regions in the background (normal) data set |
RDFV |
Raw depths of the bed regions in the foreground |
RDFA |
Median raw depth over all regions in the foreground |
RDBV |
Raw depths of the bed regions in the background |
RDBA |
Median raw depth over all regions in the background |
MU |
Mappability list of the bed regions. 1 if the mappability is one; otherwise, 0. |
The Last Column
| ID |
Description |
CNVTYPE |
Amplification / Neutral / Loss |
GT |
MEANINGLESS. Genotype. |
CN |
R of logR: 2logR |
(2) Call Table for Genes
- 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.
- These calls are determined by our criteria that summarize segment calls.
-
Columns to be explained:
| Column |
Description |
ID |
MEANINGLESS |
QUAL |
MEANINGLESS |
FILTER |
Please use calls with PASS. |
INFO Column
| ID |
Description |
SVTYPE |
Type of structural variant (CNV). |
END |
End position of the gene |
SVLEN |
Gene length |
GENE |
Gene name |
The Last Column
| ID |
Description |
CNVTYPE |
Amplification / Neutral / Loss |
BGDP |
Median raw depth over the gene in the background |
AMPLOGR |
Log R ratio of amplification segments included in the gene |
NEULOGR |
Log R ratio of neutral segments included in the gene |
LOSSLOGR |
Log R ratio of loss segments included in the gene |
AMPCOV |
Coverage of amplification segments over the gene |
NEUCOV |
Coverage of neutral segments over the gene |
LOSSCOV |
Coverage of loss segments over the gene |