Fusion calling in DNA¶
See the fusions hydra-genetics module documentation for more details on the softwares for fusion calling. Default hydra-genetics settings/resources are used if no configuration is specified.
Pipeline output files:¶
results/dna/{sample}_{type}/fusion/{sample}_{type}.gene_fuse_report.tsv(with UMI option only)results/dna/{sample}_{type}/fusion/{sample}_{type}.fuseq_wes.report.csv
Fusions calling using GeneFuse¶
DNA fusion calling is performed by GeneFuse v0.6.1 on fastq-files. It uses a gene transcript target file to limit the number of targets to analyze.
Configuration¶
References
- Fasta reference genome
- Gene transcript file with genomic positions for all exons include in the analysis
Cluster resources
| Options | Value |
|---|---|
| mem_mb | 36864 |
| mem_per_cpu | 6144 |
| threads | 6 |
| time | "8:00:00" |
GeneFuse Filtering and report¶
The output from GeneFuse is filtered and then reported into a fusion report using the in-house script report_gene_fuse.py (rule and config). The following filter criteria is used:
- Fusions must have at least 6 unique supporting reads.
- Very noisy fusion pairs found in almost all samples (defined in
filter_fusions_20230214.csv) are removed:- NPM1::ALK
- CLTC::NTRK3
- MSH2_ALK
- MSH2_HIP1
- Noisy fusion pairs found in some samples (defined in
filter_fusions_20230214.csv) are filtered individually on the number of uniquely supporting reads:- LMNA::EZR 9
- ABL1::STRN 7
- EZR::ALK 8
- RSPO2::BRAF 8
- LMNA::HIP1 12
- NPM1::BICC1 11
- RSPO2::ERG 13
Result file¶
results/dna/{sample}_{type}/fusion/{sample}_{type}.gene_fuse_report.tsv
Fusions calling using FuSeq_WES¶
DNA fusion calling is performed by FuSeq_WES v1.0.1 on bam-files. It uses a gene transcript target file to limit the number of targets to analyze.
Configuration¶
References
Software settings
| Options | Value | Description |
|---|---|---|
| params | cnv_amplfication_genes.tsv |
Genes and surrounding regions to call small CNVs in |
Cluster resources
| Options | Value |
|---|---|
| mem_mb | 12288 |
| mem_per_cpu | 6144 |
| threads | 2 |
| time | "24:00:00" |
FuSeq_WES Filtering and report¶
The output from FuSeq_WES is filtered and then reported into a fusion report using the in-house script filter_report_fuseq_wes.py (rule and config). The following filter criteria is used:
Configuration¶
Software settings
| Options | Value | Description |
|---|---|---|
| filter_on_fusiondb | True | Only keep fusions found in the fusion database |
| gene_white_list | fuseq_wes_gene_white_list.txt |
Only keep fusions with at least one gene in the gene white list |
| gene_fusion_black_list | false_positive_fusion_pairs.txt |
Remove fusions pairs in fusion pair gene black list |
| gtf | hg19.refGene.gtf |
Transcript annotation |
| min_support | 30 | Minimal total number of supporting reads |
| transcript_black_list | fuseq_wes_transcript_black_list.txt |
Transcripts that should not be used in annotation |
Result file¶
results/dna/{sample}_{type}/fusion/{sample}_{type}.fuseq_wes_report.tsv
Fusions calling using JuLI¶
Fusion calling for ctDNA is performed by JuLI. The process involves:
1. Calling: Call fusions in DNA data.
2. Annotation: Annotate fusions called by JuLI.
3. Filtering: Filter fusions using the in-house script filter_juli.py.
Result file¶
results/dna/{sample}_{type}/fusion/{sample}_{type}.juli.filtered.fusions.txt