Contents of the output/ Directory

Running cisFusion creates output/<SAMPLE_NAME>.<PANEL>/ 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_dup.vcf * Call table for genes (vcf format)
gene.cnv_wgenome_dup.txt * Call table for genes (tsv format)
seg.cnv_wgenome_dup.vcf * Call table for target bed regions (vcf format)
bed.cnv_wgenome_dup.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
  • * File names may be slightly different depending on the options of cisCall.

(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
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
GT MEANINGLESS. Genotype.
CN R of logR: 2logR
  • The tsv file in the same directory has (almost) the same contents but the format may be more useful in some cases.

(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.
  • Only amplifications are determined for the reasons described in the accompanying paper.
  • 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 Amplified / NotAmplified
LOGR DO NOT USE.
BGDP Median raw depth over the gene in the background
AMPLOGR Log R ratio of amplified segments included in the gene
NEULOGR Log R ratio of neutral segments included in the gene
DELLOGR Log R ratio of deleted segments included in the gene
AMPCOV Coverage of amplified segments over the gene
NEUCOV Coverage of neutral segments over the gene
DELCOV Coverage of deleted segments over the gene
  • The tsv file in the same directory has (almost) the same contents but the format may be more useful in some cases.