File Info

Filename
control_metrics.csv
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/32f7ef846bb980d69eef725c6343d9/control_metrics.csv
Size
5.7 KB
Task
DAQ:CONTROL_METRICS:MERGE_CONTROL_METRICS (merge_control_metrics)
Attempt

Content

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control_type sample_id variant_type qc_metric_name qc_value
germline HCC1395_BL cnv germline_control_cnv_abnormal_ploidy false
germline HCC1395_BL cnv germline_control_cnv_abnormal_ploidy_chromosomes NONE
germline HCC1395_BL cnv germline_control_cnv_del_dup_pass_ratio NA
germline HCC1395_BL cnv germline_control_cnv_del_pass_count 1
germline HCC1395_BL cnv germline_control_cnv_dup_pass_count 0
germline HCC1395_BL cnv germline_control_cnv_landmark_del_missed UGT2B17;UGT2B28
germline HCC1395_BL cnv germline_control_cnv_landmark_del_recovered_count 0
germline HCC1395_BL cnv germline_control_cnv_landmark_del_truth_total 2
germline HCC1395_BL cnv germline_control_cnv_qc_failed false
germline HCC1395_BL cnv germline_control_cnv_ugt2b17_del_cn NA
germline HCC1395_BL cnv germline_control_cnv_ugt2b17_del_filter NOT_CALLED
germline HCC1395_BL cnv germline_control_cnv_ugt2b28_del_cn NA
germline HCC1395_BL cnv germline_control_cnv_ugt2b28_del_filter NOT_CALLED
germline HCC1395_BL snv_indel germline_control_snv_indel_giab_missed_variants chr11:78079607:T:C;chr12:14928963:A:C;chr13:101721213:A:T;chr14:20060200:G:T;chr19:14799626:C:T;chr19:43848513:T:C;chr2:184937028:A:G;chr4:122894207:T:C;chr4:168448702:A:T;chr5:120686124:G:A;chr7:102934552:TGAA:T;chr9:94606867:C:T
germline HCC1395_BL snv_indel germline_control_snv_indel_giab_recovered_count 0
germline HCC1395_BL snv_indel germline_control_snv_indel_giab_truth_total 12
germline HCC1395_BL snv_indel germline_control_snv_indel_indel_count 14
germline HCC1395_BL snv_indel germline_control_snv_indel_snv_count 312
negative_somatic HCC1395_BL mimsi negative_somatic_control_mimsi_lci NA
negative_somatic HCC1395_BL mimsi negative_somatic_control_mimsi_max_msi_score NA
negative_somatic HCC1395_BL mimsi negative_somatic_control_mimsi_mean_msi_score NA
negative_somatic HCC1395_BL mimsi negative_somatic_control_mimsi_min_msi_score NA
negative_somatic HCC1395_BL mimsi negative_somatic_control_mimsi_msi_status NA
negative_somatic HCC1395_BL mimsi negative_somatic_control_mimsi_uci NA
negative_somatic HCC1395_BL msi negative_somatic_control_msi_total_sites 0
negative_somatic HCC1395_BL msi negative_somatic_control_msi_unstable_pct 0.00
negative_somatic HCC1395_BL msi negative_somatic_control_msi_unstable_sites 0
negative_somatic HCC1395_BL snv_indel negative_somatic_control_snv_indel_indel_count 0
negative_somatic HCC1395_BL snv_indel negative_somatic_control_snv_indel_snv_count 0
negative_somatic HCC1395_BL tmb negative_somatic_control_tmb_effective_coding_region_size 34.15
negative_somatic HCC1395_BL tmb negative_somatic_control_tmb_non_synonymous_count 0
negative_somatic HCC1395_BL tmb negative_somatic_control_tmb_score 0.0
positive_somatic HCC1395_tumor mimsi positive_somatic_control_mimsi_lci NA
positive_somatic HCC1395_tumor mimsi positive_somatic_control_mimsi_max_msi_score NA
positive_somatic HCC1395_tumor mimsi positive_somatic_control_mimsi_mean_msi_score NA
positive_somatic HCC1395_tumor mimsi positive_somatic_control_mimsi_min_msi_score NA
positive_somatic HCC1395_tumor mimsi positive_somatic_control_mimsi_msi_status NA
positive_somatic HCC1395_tumor mimsi positive_somatic_control_mimsi_uci NA
positive_somatic HCC1395_tumor msi positive_somatic_control_msi_total_sites 0
positive_somatic HCC1395_tumor msi positive_somatic_control_msi_unstable_pct 0.00
positive_somatic HCC1395_tumor msi positive_somatic_control_msi_unstable_sites 0
positive_somatic HCC1395_tumor snv_indel positive_somatic_control_snv_indel_coa_missed_variants PINNED_PAX7_3UTR_indel_benchmark;13655;PINNED_CDK6_3UTR_indel_benchmark;13983;376002
positive_somatic HCC1395_tumor snv_indel positive_somatic_control_snv_indel_coa_recovered_count 0
positive_somatic HCC1395_tumor snv_indel positive_somatic_control_snv_indel_coa_truth_total 5
positive_somatic HCC1395_tumor snv_indel positive_somatic_control_snv_indel_indel_count 0
positive_somatic HCC1395_tumor snv_indel positive_somatic_control_snv_indel_snv_count 0
positive_somatic HCC1395_tumor tmb positive_somatic_control_tmb_effective_coding_region_size 34.15
positive_somatic HCC1395_tumor tmb positive_somatic_control_tmb_non_synonymous_count 0
positive_somatic HCC1395_tumor tmb positive_somatic_control_tmb_score 0.0
positive_somatic Sig_18_tissue mimsi positive_somatic_control_mimsi_lci NA
positive_somatic Sig_18_tissue mimsi positive_somatic_control_mimsi_max_msi_score NA
positive_somatic Sig_18_tissue mimsi positive_somatic_control_mimsi_mean_msi_score NA
positive_somatic Sig_18_tissue mimsi positive_somatic_control_mimsi_min_msi_score NA
positive_somatic Sig_18_tissue mimsi positive_somatic_control_mimsi_msi_status NA
positive_somatic Sig_18_tissue mimsi positive_somatic_control_mimsi_uci NA
positive_somatic Sig_18_tissue msi positive_somatic_control_msi_total_sites 0
positive_somatic Sig_18_tissue msi positive_somatic_control_msi_unstable_pct 0.00
positive_somatic Sig_18_tissue msi positive_somatic_control_msi_unstable_sites 0
positive_somatic Sig_18_tissue snv_indel positive_somatic_control_snv_indel_coa_missed_variants PINNED_PAX7_3UTR_indel_benchmark;13655;PINNED_CDK6_3UTR_indel_benchmark;13983;376002
positive_somatic Sig_18_tissue snv_indel positive_somatic_control_snv_indel_coa_recovered_count 0
positive_somatic Sig_18_tissue snv_indel positive_somatic_control_snv_indel_coa_truth_total 5
positive_somatic Sig_18_tissue snv_indel positive_somatic_control_snv_indel_indel_count 0
positive_somatic Sig_18_tissue snv_indel positive_somatic_control_snv_indel_snv_count 0
positive_somatic Sig_18_tissue tmb positive_somatic_control_tmb_effective_coding_region_size 34.15
positive_somatic Sig_18_tissue tmb positive_somatic_control_tmb_non_synonymous_count 0
positive_somatic Sig_18_tissue tmb positive_somatic_control_tmb_score 0.0
67 rows