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test_data_summary.txt
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test_data_summary.txt
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| File Name: | Description: | Made from: | Using: | Needed for: |
| --- | --- | --- | --- | --- |
| tumor_normal_call.vcf.gz | Output vcf of mutect2 tumor_normal mode | test + test2 recal bams | mutect2 | filtermutectcalls |
| tumor_normal_call.vcf.gz.tbi | Index for vcf t/n | test + test2 recal bams | mutect2 | filtermutectcalls |
| tumor_normal_call.f1r2.tar.gz | Output table from mutect2 tumor_normal mode | test + test2 recal bams | mutect2 | learnreadorientationmdl |
| test2.pileups.table | Summarises tumor allele counts | test2 recal bam | GetPileupSummaries | calculatecontamination |
| test.pileups.table | Summarises normal allele counts | test recal bam | GetPileupSummaries | calculatecontamination |
| test_tumor_normal_call.artifact-prior.tar.gz | Table of artifact priors | test_tumor_normal_call.f1r2.tar.gz | learnreadorientationmdl | filtermutectcalls |
| tumor_normal_contamination.table | Table of contamination estimates | test + test2 pileups | CalculateContamination | filtermutectcalls |
| tumor_normal_segmentation.table | Table of tumor segmentations | test + test2 pileups | CalculateContamination | filtermutectcalls |
| test_genomicsdb | Genomicsdb workspace (directory) | test.genome.vcf | genomicsdbimport | genomicsdbimport, createsompon|