Contents of the output/ Directory

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

Directory Name Description
Fusion/ cisFusion output
Param/ Parameter information
Session/ Session information for IGV

Fusion/ contains the following files:

File Name Description
AlnWgenome_LmtOneside_Paired.vcf Call table (VCF format)
AlnWgenome_LmtOneside_Paired.txt Call table (TSV format)
AlnWgenome_LmtOneside_Paired_sv.vcf SV Call table (VCF format)
AlnWgenome_LmtOneside_Paired_sv.txt SV Call table (TSV format)
AlnWgenome_LmtOneside_Detail.txt Detailed call table

Output Format of the Call and SV Call Tables (VCF File)

  • Output VCF file is based on VCF format 4.2.
  • 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
    ALT Encoding of the fusion (structural variant). The outside letter of [ … [ or ] …] represents the reference nucleotide at the position. The inside represents the start position of the partner. Together, they represent upstream or downstream to the breakpoint. Refer to VCF format 4.2.
    QUAL MEANINGLESS
    FILTER Please use calls with PASS.

INFO Column

ID Description
SVTYPE Type of structural variant (BND)
MATEID ID of the partner
CIPOS Width of the estimated breakpoint due to sequence ambiguity (arising from the identical sequence of GENE1 and GENE 2 around the breakpoint). ‘L,R’ represents –L and +R from the estimated breakpoint position, POS
FTYPE Strand information of fusion genes
GENE1 Name of GENE1 at this position
GENE2 Name of GENE2 of the partner
PC Number of fusion reads of high quality in the Paired-End method
PFC Number of fusion reads of low quality in the Paired-End method
TMC Number of fusion reads of high quality in the Two-Map method
TMFC Number of fusion reads of low quality in the Two-Map method
TMEC Number of fusion reads of high quality in the Extend method, where the matches of soft clips are checked against the partner’s sequence
TMEFC Number of fusion reads of low quality in the Extend method
TC Total number of fusion reads of high quality over all the methods
FC Total number of fusion reads of low quality over all the methods
AF Fusion VAF: TC / (TC + NF)
MM Max mapping quality of fusion reads
TS Total score: TC / (median depth over target regions * 10000)
NF Number of non-fusion reads of high quality
FNF Number of non-fusion reads of low quality
FX Number of reads with low quality mutched to fusion region about soft clip
BG_PC Number of background fusion reads of high quality in the Paired-End method
BG_PFC Number of background fusion reads of low quality in the Paired-End method
BG_TMC Number of background fusion reads of high quality in the Two-Map method
BG_TMFC Number of background fusion reads of low quality in the Two-Map method
BG_TMEC Number of background fusion reads of high quality in the Extend method, where the matches of soft clips are checked against the partner’s sequence
BG_TMEFC Number of background fusion reads of low quality in the Extend method
BG_TC Total number of background fusion reads of high quality over all the methods
BG_FC Total number of background fusion reads of low quality over all the methods
BG_AF Fusion background VAF: TC / (TC + NF)
BG_MM Max mapping quality of background fusion reads
BG_TS Total score: BG_TC / (median depth over target regions * 10000)
BG_NF Number of background non-fusion reads of high quality
BG_FNF Number of background non-fusion reads of low quality
BG_FX Number of background reads with low quality mutched to fusion region about soft clip
VOR Variant Odds Ratio
FPV Fisher p-value

The Last Column

ID Description
GT MEANIGLESS. Genotype.
DPADJ TC | NF regarding GENE1