Input and Output

Inputs

  • fragment file or Cell Ranger matrix directory; when using a fragment file, the workflow sorts it internally by barcode and genomic position by default

  • reference genome FASTA

  • blacklist BED file

Outputs

  • outdir/outs/result_table.tsv.gz with the consensus Holmes+Watson CNV table

  • outdir/count_matrix.h5ad with the filtered count matrix used for inference

  • outdir/parameter_configuration.txt with the run configuration

  • outdir/binned_genome.csv with the genome bins and GC annotations

  • outdir/breakpoints.csv with the detected breakpoints per cell

  • outdir/clusters.json with the inferred segment clusters per cell

  • outdir/outs/Karyogram.png when plotting is enabled

  • outdir/outs/integer_states.tsv.gz with integer CNV states

  • outdir/outs/continuous_scores.tsv.gz with continuous CNV scores

  • outdir/outs/result_table_holmes.tsv.gz with Holmes-mapped CNV states

  • outdir/outs/result_table_watson.tsv.gz with Watson-mapped CNV states

  • outdir/outs/scaling_factors.tsv.gz with per-cell scaling factors