To Index
cisCall Parameters
1. cisMuton
The cisMuton parameters are set in param/${GROUP}.0.txt under the cisMuton execution directory by the procedure of setting parameters.
See the Setting Parameters section for the procedure.
| Parameter | Values (for Illumina and FFPE) |
|---|---|
| Fusion.2map.1.Tools | aln |
| Fusion.2map.2.Tools | bwasw |
| Fusion.2map.Source | fastq |
| Fusion.VFusion.1.Tools | aln |
| Fusion.VFusion.2.Tools | none |
| Fusion.VFusion.Source | fastq |
| Muton.M02_AccuCall | 0.001, 10, 5, 20 |
| Muton.M01.BaseQ | 15 |
| Muton.M02A.BaseQBinom.enable.del | 0 |
| Muton.M02A.BaseQBinom.enable.ins | 0 |
| Muton.M02A.BaseQBinom.enable.snv | 0 |
| Muton.M02A.BaseQBinom.prop.del | 0.8 |
| Muton.M02A.BaseQBinom.prop.ins | 0.8 |
| Muton.M02A.BaseQBinom.prop.snv | 0.8 |
| Muton.M02A.BaseQBinom.pvalue.del | 0.05 |
| Muton.M02A.BaseQBinom.pvalue.ins | 0.05 |
| Muton.M02A.BaseQBinom.pvalue.snv | 0.05 |
| Muton.M02A.BaseQdropedBias | 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 |
| Muton.M03_BetaFilter | 1, 0.25, 0.1 |
| Muton.M03_BetaFilter.Range.indel | 0.05, 0.10 |
| Muton.M03_BetaFilter.Range.snv | 0.05, 0.05 |
| Muton.M03_BnmFilter.indel | 0.05, 0.001, 0 |
| Muton.M03_BnmFilter.snv | 0.03, 0.001, 0 |
| Muton.M02A.Correlation | 1, binom, 0.5, 0.01 |
| Muton.INDEL.1.Tools | aln |
| Muton.INDEL.2.Tools | none |
| Muton.INDEL.Source | bam, fastq |
| Muton.M02A.LocalBias.bias.del | 5 |
| Muton.M02A.LocalBias.bias.ins | 5 |
| Muton.M02A.LocalBias.bias.snv | 10 |
| Muton.M02A.LocalBias.enable.del | 1 |
| Muton.M02A.LocalBias.enable.ins | 1 |
| Muton.M02A.LocalBias.enable.snv | 1 |
| Muton.M02A.LocalBinom.enable.del | 1 |
| Muton.M02A.LocalBinom.enable.ins | 1 |
| Muton.M02A.LocalBinom.enable.snv | 1 |
| Muton.M02A.LocalBinom.hetelo.del | 1 |
| Muton.M02A.LocalBinom.hetelo.ins | 1 |
| Muton.M02A.LocalBinom.hetelo.snv | 0 |
| Muton.M02A.LocalBinom.prop.all.del | 0.001 |
| Muton.M02A.LocalBinom.prop.all.ins | 0.001 |
| Muton.M02A.LocalBinom.prop.all.snv | 0.1 |
| Muton.M02A.LocalBinom.prop.alt.del | 0.001 |
| Muton.M02A.LocalBinom.prop.alt.ins | 0.001 |
| Muton.M02A.LocalBinom.prop.alt.snv | 0.05 |
| Muton.M02A.LocalBinom.pvalue.del | 1e-20, 1e-20, 1e-20 |
| Muton.M02A.LocalBinom.pvalue.ins | 1e-20, 1e-20, 1e-20 |
| Muton.M02A.LocalBinom.pvalue.snv | 1e-20, -1, -1 |
| Muton.M02A.LongHomopolymer | 1, 15, 15, 11, 11 |
| Muton.M01.MapQ | 1 |
| Muton.M02A.MisAlignment.Negative.Any | 0 |
| Muton.M02A.MisAlignment.Negative.Cross | 0 |
| Muton.M02A.MisAlignment.Positive.Any | 1, 0.001, 0.10 |
| Muton.M02A.MisAlignment.Positive.Cross | 1, 0.001, 0.10 |
| Muton.M02B.MismatchRate | 0.01, 0.01, 3, 0 |
| Muton.M02A.RemoveSNVnearINDEL | 0, 0.05 |
| Muton.SNV.1.Tools | aln |
| Muton.SNV.2.Tools | none |
| Muton.SNV.Source | bam, fastq |
| Muton.M02A.StrandBias | 0.00001 |
| Muton.M02B.Trim | 0.3333, 0 |
| Muton.M02A.ZeroMapQ | 1, 0.1, 0.1 |
2. cisFusion
The cisFusion parameters are set in param/${GROUP}.0.txt under the cisFusion execution directory by the procedure of setting parameters.
See the Setting Parameters section for the procedure.
| Parameter | Values (for Illumina and FFPE) |
|---|---|
| Muton.M02_AccuCall | 0.001, 10, 5, 20 |
| Muton.M01.BaseQ | 15 |
| Muton.M02A.LocalQBinom.enable.del | 1 |
| Muton.M02A.LocalQBinom.enable.ins | 1 |
| Muton.M02A.LocalQBinom.enable.snv | 1 |
| Muton.M02A.LocalQBinom.prop.del | 0.03 |
| Muton.M02A.LocalQBinom.prop.ins | 0.03 |
| Muton.M02A.LocalQBinom.prop.snv | 0.03 |
| Muton.M02A.LocalQBinom.hetelo.del | 1 |
| Muton.M02A.LocalQBinom.hetelo.ins | 1 |
| Muton.M02A.LocalQBinom.hetelo.snv | 0 |
| Muton.M02A.LocalQBinom.quantile.del | 0.05 |
| Muton.M02A.LocalQBinom.quantile.ins | 0.05 |
| Muton.M02A.LocalQBinom.quantile.snv | 0.05 |
| Muton.M02A.BaseQdropedBias | 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 |
| Muton.M03_BetaFilter | 1, 0.2, 0.1 |
| Muton.M03_BetaFilter.Range.indel | 0.05, 0.10 |
| Muton.M03_BetaFilter.Range.snv | 0.05, 0.05 |
| Muton.M03_BnmFilter.indel | 0.05, 0.001, 0 |
| Muton.M03_BnmFilter.snv | 0.03, 0.001, 0 |
| Muton.M02A.Correlation | 1, binom, 0.5, 0.01 |
| Muton.INDEL.Source | bam, fastq:global |
| Muton.M02A.LocalBias.bias.del | 5 |
| Muton.M02A.LocalBias.bias.ins | 5 |
| Muton.M02A.LocalBias.bias.snv | 10 |
| Muton.M02A.LocalBias.enable.del | 1 |
| Muton.M02A.LocalBias.enable.ins | 1 |
| Muton.M02A.LocalBias.enable.snv | 1 |
| Muton.M02A.LocalBinom.enable.del | 1 |
| Muton.M02A.LocalBinom.enable.ins | 1 |
| Muton.M02A.LocalBinom.enable.snv | 1 |
| Muton.M02A.LocalBinom.hetelo.del | 1 |
| Muton.M02A.LocalBinom.hetelo.ins | 1 |
| Muton.M02A.LocalBinom.hetelo.snv | 0 |
| Muton.M02A.LocalBinom.prop.del | 0.0001 |
| Muton.M02A.LocalBinom.prop.ins | 0.0001 |
| Muton.M02A.LocalBinom.prop.snv | 0.005 |
| Muton.M02A.LocalBinom.pvalue.del | 1e-20, 1e-20, 1e-20 |
| Muton.M02A.LocalBinom.pvalue.ins | 1e-20, 1e-20, 1e-20 |
| Muton.M02A.LocalBinom.pvalue.snv | 1e-20, -1, -1 |
| Muton.M02A.LongHomopolymer | 1, 15, 15, 11, 11 |
| Muton.M01.MapQ | 1 |
| Muton.M02A.MisAlignment.Negative.Any | 0 |
| Muton.M02A.MisAlignment.Negative.Cross | 0 |
| Muton.M02A.MisAlignment.Positive.Any | 1, 0.001, 0.05 |
| Muton.M02A.MisAlignment.Positive.Cross | 1, 0.001, 0.05 |
| Muton.M02B.MismatchRate | 0.01, 0.01, 3, 0 |
| Muton.M02A.RemoveSNVnearINDEL | 0, 0.05 |
| Muton.SNV.Source | bam, fastq:global |
| Muton.Source | bam, fastq:global |
| Muton.M02A.StrandBias | 0.00001 |
| Muton.M02B.Trim | 0.3333, 0 |
| Muton.M02A.ZeroMapQ | 1, 0.1, 0.1 |
3. cisCton
The parameters of cisCton are defined in ciscton/paramfactory.py.
| Parameter | Description | Value |
|---|---|---|
| gc_between | GC content calculation range | 20000 |
| stitching_size | Window size for circular binary segmentation | 160 |
| cnv_bootstrap_number | Bootstrap number to decide CNA types | 100000 |
| effect_size_divide | Effect size threshold to detect segments by circular binary segmentation | 0.05 |
| effect_size_edge | Effect size threshold to divde centers and edges by circular binary segmentation | 0.05 |
| pvalue_divide | Pvalue threshold to detect segment by circular binary segmentation | 0.05 |
| pvalue_edge | Pvalue threshold to divide centers and edges by circular binary segmentation | 0.05 |
| effect_size_cnv_decision | Effect size threshold to decide CNA types | 1 |
| pvalue_cnv_decision | Pvalue threshold to decide CNA types | 0.0001 |
| gene_cover_rate | Minimum coverage to decide CNA types for genes | 0.8 |
| mapability | Minimum mappability for baseline regions | 0.99 |
| min_amplified | Minimum log R ratio for amplifications | 2 |
| diff_logr_abnormal_segment | Minimum difference of log R ratio for abnormal segments | 1 |
| over_ratio_abnormal_segment | Minimum abnormal logR ratio for abnormal segments | 0.2 |