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Merge pull request #17 from eastgenomics/refactor
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update output paths in readme (#17)
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@Aisha-D
Aisha-D authored Nov 10, 2023
2 parents 0a5ceb0 + aea6b77 commit ae56337
Showing 1 changed file with 15 additions and 15 deletions.
30 changes: 15 additions & 15 deletions README.md
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Expand Up @@ -39,21 +39,21 @@ 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 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/*/*` | 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 files |
| `metricsOutput` | TSV | `/Results/Results/` | Final MetricsOutput TSV file for the run |
| `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 |
| `fastqs` | FASTQ | `/demultiplexOutput/Logs_Intermediates/FastqGeneration/` | The FASTQs as output from bclconvert |
| `dna_bams` | BAM | `/scatter/StitchedRealigned/*/` | The 'final' BAM files upon which variant calling is performed |
| `dna_bam_index` | BAI | `/scatter/StitchedRealigned/*/` | Index of the above BAMs |
| `rna_bam` | BAM | `/scatter/RnaAlignment/*/` | Downsampled and trimmed BAMs aligned by STAR aligner |
| `rna_bam_index` | BAI | `/scatter/RnaAlignment/*/` | Index of the above BAMs |
| `msi_metrics` | JSON | `/scatter/Msi/*/` | MSI metrics in JSON format |
| `tmb_metrics` | JSON | `/scatter/Tmb/*/` | TMB metrics in JSON format |
| `fusions` | CSV | `/gather/Results/*/` | CSVs of all identified fusions from RNA analysis |
| `small_variant_annotation` | JSON | `/gather/Results/*/` | Annotated variants in JSON |
| `splice_variant_annotation` | JSON | `/gather/Results/*/` | Annotated splice variants from RNA analysis in JSON |
| `cvo` | TSV | `/gather/Results/*/` | CombinedVariantOutput TSV files |
| `metricsOutput` | TSV | `/` | Final MetricsOutput TSV file for the run |
| `cnv_vcfs` | VCF | `/gather/Results/*/` | Final CNV VCFs from Results directory |
| `gvcfs` | VCF | `/gather/Results/*/` | Genome VCFs from the merging step |
| `splice_variants_vcf` | VCF | `/gather/Results/*/` | VCFs of splice variants from RNA analysis |



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