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update readme
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@jethror1
jethror1 committed Nov 2, 2023
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Expand Up @@ -40,20 +40,20 @@ This outputs the full TSO500 local app, including all analysis files and interme
| Field | Type | Path | Notes |
|--------------------- |------- |--------------------------------------------------------- |-------------------------------------------------------------- |
| `fastqs` | FASTQ | `/DemultiplexOutput/Logs_Intermediates/FastqGeneration` | The FASTQs as output from bclconvert |
| `dna_bams` | BAM | `/Analysis/*/Logs_Intermediates/StitchedRealigned/` | The 'final' BAM file upon which variant calling is performed |
| `dna_bam_index` | BAI | `/Analysis/*/Logs_Intermediates/StitchedRealigned/` | Index of the above BAM |
| `rna_bam` | BAM | `/Analysis/*/Logs_Intermediates/RnaAlignment/*` | Downsampled and trimmed BAM aligned by STAR aligner |
| `rna_bam_index` | BAI | `/Analysis/*/Logs_Intermediates/RnaAlignment/*` | Index of the above BAM |
| `dna_bams` | BAM | `/Analysis/*/Logs_Intermediates/StitchedRealigned/` | The 'final' BAM files upon which variant calling is performed |
| `dna_bam_index` | BAI | `/Analysis/*/Logs_Intermediates/StitchedRealigned/` | Index of the above BAMs |
| `rna_bam` | BAM | `/Analysis/*/Logs_Intermediates/RnaAlignment/*` | Downsampled and trimmed BAMs aligned by STAR aligner |
| `rna_bam_index` | BAI | `/Analysis/*/Logs_Intermediates/RnaAlignment/*` | Index of the above BAMs |
| `msi_metrics` | JSON | `/Analysis/*/Logs_Intermediates/Msi/*` | MSI metrics in JSON format |
| `tmb_metrics` | JSON | `/Analysis/*/Logs_Intermediates/Tmb/*` | TMB metrics in JSON format |
| `fusions` | CSV | `/Results/Results/*/*` | CSV of all identified fusions from RNA analysis |
| `small_variant_annotation` | JSON | `/Results/Results/*/*` | Annotated variant JSON |
| `fusions` | CSV | `/Results/Results/*/*` | CSVs of all identified fusions from RNA analysis |
| `small_variant_annotation` | JSON | `/Results/Results/*/*` | Annotated variants in JSON |
| `splice_variant_annotation` | JSON | `/Results/Results/*/*` | Annotated splice variants from RNA analysis in JSON |
| `cvo` | TSV | `/Results/Results/*/*` | CombinedVariantOutput TSV file |
| `cvo` | TSV | `/Results/Results/*/*` | CombinedVariantOutput TSV files |
| `metricsOutput` | TSV | `/Results/Results/` | Final MetricsOutput TSV file for the run |
| `cnv_vcfs` | VCF | `/Results/Results/*/*` | Final CNV VCF from Results directory |
| `gvcfs` | VCF | `/Results/Results/*/*` | Genome VCF from the merging step |
| `splice_variants_vcf` | VCF | `/Results/Results/*/*` | VCF of splice variants from RNA analysis |
| `cnv_vcfs` | VCF | `/Results/Results/*/*` | Final CNV VCFs from Results directory |
| `gvcfs` | VCF | `/Results/Results/*/*` | Genome VCFs from the merging step |
| `splice_variants_vcf` | VCF | `/Results/Results/*/*` | VCFs of splice variants from RNA analysis |



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