Outputs

This page summarizes important files generated by the current SpaceTracer workflow.

Key intermediate outputs

  • output_dir/cluster/cluster.txt and output_dir/cell_num.txt (or your configured external cell_num file) Cluster assignments and cell-number support for downstream genotype modeling. If you provide these files in config or skip early steps, these outputs may not be regenerated under output_dir.

  • output_dir/bam_processing/IN.bam, output_dir/bam_processing/IN_filter.bam In-tissue BAM and filtered BAM used by mpileup and read-level feature extraction.

  • output_dir/mpileup/raw_mpileup.txt, output_dir/mpileup/filter_mpileup.txt, output_dir/mpileup/umi_combine_chunk_manifest.tsv Raw/filter mpileup evidence and chunk manifest used by umi_combine.

  • output_dir/umi_combine/spot.count.list.csv, output_dir/umi_combine/error.count.list.csv Chunk-manifest files that point to per-chunk parquet outputs for spot/error evidence.

  • output_dir/prior.txt Prior table used in genotyping.

  • output_dir/genotyping/genotyping_chunk_manifest.tsv Per-chunk genotype outputs (for example ind_geno_filter.out, spot_geno.out, cluster_vaf.out) under output_dir/genotyping/<chunk>/.

  • output_dir/spatial_feature/<sample>/spatial_feature_chunk_manifest.tsv Spatial feature chunk outputs.

  • output_dir/read_feature/<sample>/read_feature_chunk_manifest.tsv Read-level feature chunk outputs.

  • output_dir/mappability_feature/mappability_feature.txt Mappability feature table.

  • output_dir/RNA_feature/RNA_feature.txt RNA-level feature table (with ASE/hFDR/editing-related annotations).

  • output_dir/all_feature.txt Integrated feature table produced by merge_feature.

  • output_dir/all_feature.parquet

Mutation-prediction outputs

Typical outputs from mutation_prediction are:

  • output_dir/mutation_prediction/results/Sample_total_pred_truesites.vcf
  • output_dir/mutation_prediction/results/Sample_total_pred_truesites_PASS.vcf
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
chr1    16562519    .   C   A   .   PASS    DP=196;ALT_DP=24;VAF=0.122449;NUM_SPOTS=135;NUM_MUT_SPOTS=23;DNA_MUT_TYPE=A[C>A]A;RNA_MUT_TYPE=T[G>T]T
chr1    19682510    .   G   A   .   PASS    DP=79;ALT_DP=17;VAF=0.21519;NUM_SPOTS=71;NUM_MUT_SPOTS=17;DNA_MUT_TYPE=T[C>T]T;RNA_MUT_TYPE=T[C>T]T
chr1    36393565    .   G   A   .   PASS    DP=525;ALT_DP=89;VAF=0.169524;NUM_SPOTS=368;NUM_MUT_SPOTS=79;DNA_MUT_TYPE=T[C>T]C;RNA_MUT_TYPE=T[C>T]C
chr1    46675536    .   G   A   .   PASS    DP=118;ALT_DP=20;VAF=0.160494;NUM_SPOTS=73;NUM_MUT_SPOTS=13;DNA_MUT_TYPE=G[C>T]T;RNA_MUT_TYPE=G[C>T]T
chr1    155234903   .   C   T   .   PASS    DP=39;ALT_DP=3;VAF=0.0769231;NUM_SPOTS=39;NUM_MUT_SPOTS=3;DNA_MUT_TYPE=G[C>T]T;RNA_MUT_TYPE=A[G>A]C

Visualization and validation

1) Lineage reconstruction with PhyloSOLID

After obtaining final predicted sites, you can run PhyloSOLID to infer lineage relationships.

Lineage tree example

2) Spatial probability scatter plot

SpaceTracer supports spatial visualization of mutation probability and mutant/non-mutant spot patterns.

Mutation probability scatter plot

3) IGV validation views

To manually validate candidate calls, IGV snapshots can be used to compare mutant-like and non-mutant/reference-homozygous spots.

Mutant spots

IGV mutant example

Non-mutant/reference-homozygous spots

IGV reference-homozygous example