File Info
- Filename
- variant_qc.csv
- Full Path
- s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/e1c69f2aed35bb80b4ef1dcf9d5e54/variant_qc.csv
- Size
- 1.4 KB
- Attempt
Content
View in new tab| pair_id | tumor_sample | normal_sample | contamination_normal_contamination_pct | contamination_tumor_contamination_pct | identity_matched | identity_tumor_normal_correlation | normal_deconflict_chip_germ_chip_wins | normal_deconflict_chip_germ_germ_wins | normal_deconflict_chip_germ_suppress_both | normal_deconflict_chip_somatic_suspect | normal_deconflict_germ_som_germ_wins | normal_deconflict_germ_som_suppress_both | normal_deconflict_total_chip_germ_conflicts | normal_deconflict_total_germ_som_conflicts | normal_germline_cnv_cnv_call_status | normal_germline_cnv_list_of_abnormal_ploidy_chr | normal_germline_cnv_low_coverage_sample_or_batch | normal_germline_cnv_num_del | normal_germline_cnv_num_del_abnormal_ploidy_chr | normal_germline_cnv_num_dup | normal_germline_cnv_num_dup_abnormal_ploidy_chr | normal_germline_cnv_num_lowconf_del | normal_germline_cnv_num_lowconf_del_abnormal_ploidy_chr | normal_germline_cnv_num_lowconf_dup | normal_germline_cnv_num_lowconf_dup_abnormal_ploidy_chr | strelka_num_indels | strelka_num_snps | tmb_effective_coding_region_size | tmb_filtered_variant_count | tmb_non_synonymous_count |
| HCC1395_tumor_vs_HCC1395_BL | HCC1395_tumor | HCC1395_BL | 0.007 | 0.262 | True | 0.98 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PASS | False | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 35 | 369 | 0.34 | 4.0 | 1.0 | |
| Sig_18_tissue_vs_Sig_18_Blood | 0.026 | 0.055 | ||||||||||||||||||||||||||||
| custom_Sig_18_tumor_normal | Sig_18_tissue | Sig_18_Blood | True | 0.9901 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PASS | False | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 66 | 265 | 0.34 | 5.0 | 2.0 |
4 rows