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Filename
comparison/variant_classification.tsv
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/607f16440c89581e40dbc10bad76fb/comparison/variant_classification.tsv
Size
10.9 KB
Task
VARIANT_COMPARISON_TSO500:COMPARE_VARIANTS
Attempt

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specimen_id sample_id chrom pos ref alt variant_type original_variant_type region truth_vaf pass_in_truth is_hotspot hotspot_label exp_vaf pass_in_exp classification test_vcf_status test_vcf_filter test_vcf_tumor_vaf test_vcf_tumor_dp test_vcf_tumor_ad_ref test_vcf_tumor_ad_alt test_vcf_normal_vaf test_vcf_normal_dp test_vcf_normal_ad_ref test_vcf_normal_ad_alt
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr1 119916592 G A SNV SNV boosted_exome 0.4672000110149383 True False nan 0.4749999940395355 True TP called_pass PASS 0.4749999940395355 4606 2410 2196 0.0021200000774115 1124 1123 1
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr1 158636760 C T SNV SNV boosted_exome 0.521399974822998 True False nan 0.6110000014305115 True TP called_pass PASS 0.6110000014305115 4448 1715 2733 0.0012900000438094 1001 1001 0
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr2 25743239 G A SNV SNV boosted_exome 0.5317999720573425 True False nan 0.5099999904632568 True TP called_pass PASS 0.5099999904632568 4097 2019 2078 0.000722000026144 1658 1658 0
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr2 47800285 C T SNV SNV boosted_exome 0.3411000072956085 True False nan 0.3400000035762787 True TP called_pass PASS 0.3400000035762787 2568 1691 877 0.0009069999796338 1319 1318 1
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr3 179234297 A G SNV SNV boosted_exome 0.5263000130653381 True True PIK3CA p.His1047 0.4729999899864197 True TP called_pass PASS 0.4729999899864197 3315 1734 1581 0.000304999994114 3970 3968 2
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr4 55115369 C T SNV SNV boosted_exome 0.4438999891281128 True False nan 0.3479999899864197 True TP called_pass PASS 0.3479999899864197 1202 784 418 0.0013399999588727 968 968 0
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr5 1295135 G A SNV SNV boosted_exome 0.8174999952316284 True False nan 0.8519999980926514 True TP called_pass PASS 0.8519999980926514 2336 332 2004 0.0010199999669566 1139 1138 1
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr5 56882468 A G SNV SNV boosted_exome 0.8391000032424927 True False nan 0.8289999961853027 True TP called_pass PASS 0.8289999961853027 2440 417 2023 0.001010000007227 1131 1131 0
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr6 32213715 G A SNV SNV boosted_exome 0.2373999953269958 True False nan 0.2349999994039535 True TP called_pass PASS 0.2349999994039535 4996 3810 1186 0.0008270000107586 1578 1578 0
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr6 93410659 G A SNV SNV boosted_exome 0.4469000101089477 True False nan 0.4860000014305115 True TP called_pass PASS 0.4860000014305115 4697 2417 2280 0.0007489999989047 1594 1594 0
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr6 117324413 C T SNV SNV boosted_exome 0.4377999901771545 True False nan 0.4930000007152557 True TP called_pass PASS 0.4930000007152557 1738 872 866 0.0017099999822676 1337 1336 1
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr7 140753336 A T SNV SNV boosted_exome 0.6837000250816345 True True BRAF p.Val600 0.6779999732971191 True TP called_pass PASS 0.6779999732971191 3266 1043 2223 0.0021100000012665 2476 2470 6
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr7 148827209 G A SNV SNV boosted_exome 0.226500004529953 True False nan 0.2000000029802322 True TP called_pass PASS 0.2000000029802322 1441 1158 283 0.0017800000496208 756 756 0
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr8 47840077 G A SNV SNV boosted_exome 0.2162999957799911 True False nan 0.2560000121593475 True TP called_pass PASS 0.2560000121593475 1810 1341 469 0.0016599999507889 829 829 0
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr8 68192376 G A SNV SNV boosted_exome 0.5712000131607056 True False nan 0.5929999947547913 True TP called_pass PASS 0.5929999947547913 1623 667 956 0.0027999999001622 436 436 0
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr9 125149801 G A SNV SNV boosted_exome 0.833299994468689 True False nan 0.8199999928474426 True TP called_pass PASS 0.8199999928474426 1318 244 1074 0.0011500000255182 1104 1104 0
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr12 69574155 C T SNV SNV boosted_exome 0.2960000038146972 True False nan 0.2820000052452087 True TP called_pass PASS 0.2820000052452087 4095 2961 1134 0.0007820000173524 1592 1592 0
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr12 69574155 CT TC MNV MNV boosted_exome 0.2960000038146972 True False nan False FN
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr12 69574156 T C SNV SNV boosted_exome 0.2967000007629394 True False nan 0.2820000052452087 True TP called_pass PASS 0.2820000052452087 4095 2961 1134 0.0007820000173524 1592 1592 0
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr13 101722929 C T SNV SNV boosted_exome 0.5023999810218811 True False nan 0.5299999713897705 True TP called_pass PASS 0.5299999713897705 5380 2524 2856 0.0019399999873712 1269 1267 2
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr17 40349793 C T SNV SNV boosted_exome 0.0837000012397766 True False nan 0.0995000004768371 True TP called_pass PASS 0.0995000004768371 3377 3049 328 0.0012799999676644 999 999 0
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr18 45038510 G A SNV SNV boosted_exome 0.7935000061988831 True False nan 0.8379999995231628 True TP called_pass PASS 0.8379999995231628 1773 295 1478 0.0013299999991431 948 948 0
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr19 10489778 G A SNV SNV boosted_exome 0.3007000088691711 True False nan 0.2809999883174896 True TP called_pass PASS 0.2809999883174896 3729 2683 1046 0.0010999999940395 1237 1237 0
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr19 11034992 C T SNV SNV boosted_exome 0.2737999856472015 True False nan 0.2809999883174896 True TP called_pass PASS 0.2809999883174896 4351 3139 1212 0.0016100000357255 1534 1532 2
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr19 41256496 C T SNV SNV boosted_exome 0.2813999950885772 True False nan 0.2840000092983246 True TP called_pass PASS 0.2840000092983246 3272 2333 939 0.0011800000211223 1127 1127 0
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chr20 58854030 C T SNV SNV boosted_exome 0.446399986743927 True False nan 0.4699999988079071 True TP called_pass PASS 0.4699999988079071 6598 3470 3128 0.0013999999500811 1713 1711 2
1029_05O 1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1 chrX 53195038 C T SNV SNV boosted_exome 0.1709000021219253 True False nan 0.164000004529953 True TP called_pass PASS 0.164000004529953 3865 3219 646 0.0008040000102482 1510 1510 0
1029_0DT 1029_0DT-T1-TDNA-1_23K7YCLT4_1_vs_1029_0DT-N1-BDNA-1_235YY7LT3_1 chr2 25234373 C T SNV SNV boosted_exome 0.0164000000804662 True False nan False FN called_hard_filtered normal_artifact;high_normal_vaf 0.0207000002264976 5592 5477 115 0.0847000032663345 1178 1086 92
1029_0DT 1029_0DT-T1-TDNA-1_23K7YCLT4_1_vs_1029_0DT-N1-BDNA-1_235YY7LT3_1 chr4 1806149 C T SNV SNV boosted_exome 0.0619000010192394 True False nan 0.0702999979257583 True TP called_pass PASS 0.0702999979257583 2674 2480 194 0.0010400000028312 1182 1182 0
1029_0DT 1029_0DT-T1-TDNA-1_23K7YCLT4_1_vs_1029_0DT-N1-BDNA-1_235YY7LT3_1 chr8 47779083 C G SNV SNV boosted_exome 0.0615000016987323 True False nan 0.0555999986827373 True TP called_pass PASS 0.0555999986827373 1225 1160 65 0.001700000022538 772 772 0
1029_0DT 1029_0DT-T1-TDNA-1_23K7YCLT4_1_vs_1029_0DT-N1-BDNA-1_235YY7LT3_1 chr17 48723750 G A SNV SNV nonboosted_exome 0.0153000000864267 True False nan False FN called_hard_filtered normal_artifact;high_normal_vaf 0.0105999996885657 2190 2167 23 0.0284000001847744 483 471 12
1029_0DT 1029_0DT-T1-TDNA-1_23K7YCLT4_1_vs_1029_0DT-N1-BDNA-1_235YY7LT3_1 chr19 5210563 C T SNV SNV boosted_exome 0.0388999991118907 True False nan False FN called_hard_filtered normal_artifact;high_normal_vaf 0.0544000007212162 3736 3528 208 0.1360000073909759 1173 1005 168
1029_0DT 1029_0DT-T1-TDNA-1_23K7YCLT4_1_vs_1029_0DT-N1-BDNA-1_235YY7LT3_1 chr19 11034986 G A SNV SNV boosted_exome 0.0595000013709068 True False nan 0.0740000009536743 True TP called_pass PASS 0.0740000009536743 3919 3629 290 0.0015300000086426 1408 1407 1
1029_0DT 1029_0DT-T1-TDNA-1_23K7YCLT4_1_vs_1029_0DT-N1-BDNA-1_235YY7LT3_1 chr20 32434483 T TA INDEL INDEL boosted_exome 0.0181000009179115 True False nan False FN
1029_0DT 1029_0DT-T1-TDNA-1_23K7YCLT4_1_vs_1029_0DT-N1-BDNA-1_235YY7LT3_1 chrX 77574296 A G SNV SNV boosted_exome 0.0270000007003545 True False nan False FN called_hard_filtered haplotype 0.0483999997377395 1091 1038 53 0.0020999999251216 665 665 0
1029_0DT 1029_0DT-T1-TDNA-1_23K7YCLT4_1_vs_1029_0DT-N1-BDNA-1_235YY7LT3_1 chrX 101353979 C A SNV SNV boosted_exome 0.0564999990165233 True False nan 0.0791999995708465 True TP called_pass PASS 0.0791999995708465 1911 1752 159 0.0015600000042468 837 837 0
1029_032 1029_032-T1-TDNA-1_23K7YCLT4_1_vs_1029_032-N1-BDNA-1_235YY7LT3_1 chr2 108782708 C T SNV SNV boosted_exome False False nan 0.0226000007241964 True FP called_pass PASS 0.0226000007241964 1575 1538 37 0.0009810000192373 1217 1217 0
1029_032 1029_032-T1-TDNA-1_23K7YCLT4_1_vs_1029_032-N1-BDNA-1_235YY7LT3_1 chr11 108343277 C G SNV SNV boosted_exome False False nan 0.0320999994874 True FP called_pass PASS 0.0320999994874 1426 1381 45 0.001010000007227 1344 1344 0
1029_032 1029_032-T1-TDNA-1_23K7YCLT4_1_vs_1029_032-N1-BDNA-1_235YY7LT3_1 chr13 28061918 A G SNV SNV boosted_exome False False nan 0.0226000007241964 True FP called_pass PASS 0.0226000007241964 1618 1582 36 0.0016299999551847 790 790 0
1029_032 1029_032-T1-TDNA-1_23K7YCLT4_1_vs_1029_032-N1-BDNA-1_235YY7LT3_1 chrX 44873590 T C SNV SNV boosted_exome False False nan 0.0027099999133497 True FP called_pass PASS 0.0027099999133497 9262 9115 147 0.0022599999792873 1941 1912 29
1029_0DT 1029_0DT-T1-TDNA-1_23K7YCLT4_1_vs_1029_0DT-N1-BDNA-1_235YY7LT3_1 chr2 108765171 A G SNV SNV boosted_exome False False nan 0.004139999859035 True FP called_pass PASS 0.004139999859035 2854 2842 12 0.0012700000079348 1804 1803 1
1029_0DT 1029_0DT-T1-TDNA-1_23K7YCLT4_1_vs_1029_0DT-N1-BDNA-1_235YY7LT3_1 chr3 185480362 G C SNV SNV boosted_exome False False nan 0.0052800001576542 True FP called_pass PASS 0.0052800001576542 5131 5104 27 0.0009740000241436 1253 1253 0
1029_0DT 1029_0DT-T1-TDNA-1_23K7YCLT4_1_vs_1029_0DT-N1-BDNA-1_235YY7LT3_1 chr22 21805981 G A SNV SNV boosted_exome False False nan 0.0078900000080466 True FP called_pass PASS 0.0078900000080466 1173 1163 10 0.0022700000554323 599 599 0
44 rows