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Change default min_mapping_quality to 5 for DeepVariant. Note that we…
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…'ll likely set different default for PacBio and Illumina data.

PiperOrigin-RevId: 321657570
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@pichuan @copybara-github
pichuan authored and copybara-github committed Jul 16, 2020
1 parent 73ad6f2 commit 0a0b1db
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2 changes: 1 addition & 1 deletion deepvariant/make_examples.py
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'only be considered if all bases in the allele have a quality greater than '
'min_base_quality.')
flags.DEFINE_integer(
'min_mapping_quality', 10,
'min_mapping_quality', 5,
'By default, reads with any mapping quality are kept. Setting this field '
'to a positive integer i will only keep reads that have a MAPQ >= i. Note '
'this only applies to aligned reads.')
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156 changes: 78 additions & 78 deletions deepvariant/testdata/golden.postprocess_gvcf_output.g.vcf
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156 changes: 78 additions & 78 deletions deepvariant/testdata/golden.postprocess_single_site_output.vcf
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##DeepVariant_version=1.0.0
##contig=<ID=chr20,length=63025520>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr20 10000117 . C T 43.4 PASS . GT:GQ:DP:AD:VAF:PL 0/1:42:55:25,30:0.545455:43,0,48
chr20 10000211 . C T 47.9 PASS . GT:GQ:DP:AD:VAF:PL 0/1:47:59:30,29:0.491525:47,0,55
chr20 10000439 . T G 35.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:35:72:0,72:1:35,42,0
chr20 10000598 . T A 55.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:51:46:0,46:1:55,52,0
chr20 10000694 . G A 11.6 PASS . GT:GQ:DP:AD:VAF:PL 0/1:11:48:26,22:0.458333:11,0,22
chr20 10000758 . T A 42.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:39:56:0,56:1:42,41,0
chr20 10001019 . T G 1 RefCall . GT:GQ:DP:AD:VAF:PL ./.:7:44:31,13:0.295455:0,5,24
chr20 10001298 . T A 41.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:39:43:0,43:1:41,41,0
chr20 10001436 . A AAGGCT 43.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:43:39:2,35:0.897436:43,50,0
chr20 10001474 . C T 46.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:44:36:0,36:1:46,47,0
chr20 10001617 . C A 35.5 PASS . GT:GQ:DP:AD:VAF:PL 0/1:36:43:23,20:0.465116:35,0,55
chr20 10001628 . G A 49.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:44:0,44:1:49,52,0
chr20 10001661 . T C 58 PASS . GT:GQ:DP:AD:VAF:PL 1/1:57:47:0,47:1:58,62,0
chr20 10001670 . T G 57.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:54:46:0,46:1:57,56,0
chr20 10002058 . T G 51.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:47:58:0,58:1:51,48,0
chr20 10002099 . C T 48.8 PASS . GT:GQ:DP:AD:VAF:PL 0/1:47:57:27,30:0.526316:48,0,51
chr20 10002138 . C G 60.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:59:47:0,47:1:60,63,0
chr20 10002142 . G C 58.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:56:47:0,47:1:58,59,0
chr20 10002457 . AG A 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:39:44:40,4:0.0909091:0,39,48
chr20 10002458 . G GTT,GTTT 33.7 PASS . GT:GQ:DP:AD:VAF:PL 1/2:10:51:2,27,15:0.529412,0.294118:33,29,10,29,0,21
chr20 10002470 . C T 32.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:32:42:0,42:1:32,38,0
chr20 10002493 . A C 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:51:37:32,5:0.135135:0,52,58
chr20 10002625 . G T 52.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:47:55:0,55:1:52,47,0
chr20 10003021 . C T 50 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:38:0,38:1:49,51,0
chr20 10003109 . A C 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:54:32:28,4:0.125:0,54,62
chr20 10003358 . A C 44.3 PASS . GT:GQ:DP:AD:VAF:PL 0/1:44:51:24,27:0.529412:44,0,51
chr20 10003651 . T C 53.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:49:44:0,44:1:53,50,0
chr20 10003692 . A G 57.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:55:44:0,44:1:57,58,0
chr20 10003832 . G A 52.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:47:37:0,37:1:52,48,0
chr20 10004094 . A C 50.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:35:0,35:1:50,52,0
chr20 10004147 . A G 53.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:41:0,41:1:53,49,0
chr20 10004193 . G T 47.1 PASS . GT:GQ:DP:AD:VAF:PL 0/1:45:42:19,21:0.5:47,0,49
chr20 10004222 . C CA 41.2 PASS . GT:GQ:DP:AD:VAF:PL 0/1:35:50:20,28:0.56:41,0,35
chr20 10004223 . A AG 25.1 PASS . GT:GQ:DP:AD:VAF:PL 0/1:25:54:39,15:0.277778:25,0,37
chr20 10004253 . A T 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:55:55:48,7:0.127273:0,55,61
chr20 10004351 . C G 52.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:50:50:0,50:1:52,53,0
chr20 10004389 . T G 52 PASS . GT:GQ:DP:AD:VAF:PL 1/1:47:41:0,41:1:52,49,0
chr20 10004610 . A C 42 PASS . GT:GQ:DP:AD:VAF:PL 1/1:41:51:0,51:1:41,47,0
chr20 10004725 . A G 34.1 PASS . GT:GQ:DP:AD:VAF:PL 0/1:34:51:27,24:0.470588:34,0,44
chr20 10004769 . TAAAACTATGC T 29.1 PASS . GT:GQ:DP:AD:VAF:PL 0/1:15:53:14,39:0.735849:28,0,14
chr20 10004874 . A C 33.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:32:58:0,58:1:33,36,0
chr20 10004887 . A G 28 PASS . GT:GQ:DP:AD:VAF:PL 0/1:28:57:30,27:0.473684:27,0,38
chr20 10005010 . C T 52 PASS . GT:GQ:DP:AD:VAF:PL 1/1:49:54:0,54:1:52,52,0
chr20 10005427 . C T 45.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:44:44:0,44:1:45,48,0
chr20 10005499 . A G 51.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:49:45:0,45:1:51,51,0
chr20 10005587 . A G 41.5 PASS . GT:GQ:DP:AD:VAF:PL 0/1:40:61:31,30:0.491803:41,0,45
chr20 10005723 . A G 48.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:53:0,53:1:48,55,0
chr20 10006291 . G A 24.1 PASS . GT:GQ:DP:AD:VAF:PL 0/1:24:55:29,26:0.472727:24,0,42
chr20 10006404 . A C 52.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:49:50:0,50:1:52,51,0
chr20 10006682 . T A 39.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:39:47:0,47:1:39,46,0
chr20 10006819 . AAAAC A 48.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:42:44:0,44:1:48,43,0
chr20 10007150 . G C 38.8 PASS . GT:GQ:DP:AD:VAF:PL 0/1:39:46:29,17:0.369565:38,0,55
chr20 10007175 . C T 39.6 PASS . GT:GQ:DP:AD:VAF:PL 0/1:39:45:22,23:0.511111:39,0,50
chr20 10007352 . C T 54.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:50:45:0,45:1:54,52,0
chr20 10007531 . A G 54.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:49:51:0,51:1:54,50,0
chr20 10007980 . A C 48.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:47:61:0,61:1:48,54,0
chr20 10008029 . T TA 50.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:42:43:0,43:1:50,42,0
chr20 10008146 . TA T 46.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:42:46:0,46:1:46,44,0
chr20 10008221 . T C 52.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:50:51:0,51:1:52,53,0
chr20 10008458 . T G 48.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:42:36:0,36:1:48,42,0
chr20 10008717 . AT A 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:53:25:23,2:0.08:0,53,62
chr20 10008742 . G T 23.8 PASS . GT:GQ:DP:AD:VAF:PL 0/1:12:31:13,16:0.516129:23,0,11
chr20 10008750 . T TAA 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:47:27:21,2:0.0740741:0,47,54
chr20 10008758 . C CA 16 PASS . GT:GQ:DP:AD:VAF:PL 1/1:15:31:4,19:0.612903:15,21,0
chr20 10008921 . C CA 31.4 PASS . GT:GQ:DP:AD:VAF:PL 0/1:31:29:17,8:0.275862:31,0,53
chr20 10008948 . TA T 36.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:25:40:0,40:1:36,25,0
chr20 10008952 . CACACACACACA C,CCACACACACA 44.6 PASS . GT:GQ:DP:AD:VAF:PL 1/2:21:42:2,14,25:0.333333,0.595238:44,25,47,25,0,26
chr20 10009227 . A G 34.7 PASS . GT:GQ:DP:AD:VAF:PL 0/1:33:66:34,32:0.484848:34,0,37
chr20 10009246 . A G 46.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:42:68:0,68:1:46,44,0
chr20 10009400 . T A 37.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:35:70:0,70:1:37,38,0
chr20 10009512 . C G 52.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:45:47:0,47:1:52,46,0
chr20 10009719 . A G 57 PASS . GT:GQ:DP:AD:VAF:PL 1/1:52:33:0,33:1:56,53,0
chr20 10009795 . A G 37.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:37:40:0,40:1:37,49,0
chr20 10009844 . G A,AAGAGAGAG 13.1 PASS . GT:GQ:DP:AD:VAF:PL 1/2:3:41:6,30,5:0.731707,0.121951:10,17,0,17,0,14
chr20 10009871 . A G 36.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:34:47:5,42:0.893617:36,36,0
chr20 10009875 . A G 30.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:27:51:5,46:0.901961:30,29,0
chr20 10009879 . A G 22.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:22:48:0,48:1:22,35,0
chr20 10009883 . A G 31.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:31:50:0,50:1:31,39,0
chr20 10000117 . C T 46.3 PASS . GT:GQ:DP:AD:VAF:PL 0/1:46:55:25,30:0.545455:46,0,53
chr20 10000211 . C T 46.1 PASS . GT:GQ:DP:AD:VAF:PL 0/1:46:59:30,29:0.491525:46,0,57
chr20 10000439 . T G 45 PASS . GT:GQ:DP:AD:VAF:PL 1/1:42:72:0,72:1:44,45,0
chr20 10000598 . T A 53.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:50:46:0,46:1:53,52,0
chr20 10000694 . G A 23.2 PASS . GT:GQ:DP:AD:VAF:PL 0/1:23:48:26,22:0.458333:23,0,40
chr20 10000758 . T A 52.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:49:56:0,56:1:52,51,0
chr20 10001019 . T G 7.2 PASS . GT:GQ:DP:AD:VAF:PL 0/1:7:44:31,13:0.295455:6,0,29
chr20 10001298 . T A 45.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:36:43:0,43:1:45,36,0
chr20 10001436 . A AAGGCT 49.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:46:39:2,35:0.897436:49,48,0
chr20 10001474 . C T 52.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:50:36:0,36:1:52,52,0
chr20 10001617 . C A 35.8 PASS . GT:GQ:DP:AD:VAF:PL 0/1:36:43:23,20:0.465116:35,0,53
chr20 10001628 . G A 59.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:56:44:0,44:1:59,59,0
chr20 10001661 . T C 57.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:51:47:0,47:1:57,52,0
chr20 10001670 . T G 58.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:57:46:0,46:1:58,61,0
chr20 10002058 . T G 54.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:47:58:0,58:1:54,48,0
chr20 10002099 . C T 50.2 PASS . GT:GQ:DP:AD:VAF:PL 0/1:49:57:27,30:0.526316:50,0,54
chr20 10002138 . C G 61.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:59:47:0,47:1:61,62,0
chr20 10002142 . G C 62.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:59:47:0,47:1:62,60,0
chr20 10002457 . AG A 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:26:44:40,4:0.0909091:0,25,43
chr20 10002458 . G GTT,GTTT 33.5 PASS . GT:GQ:DP:AD:VAF:PL 1/2:9:51:2,27,15:0.529412,0.294118:33,29,8,29,0,32
chr20 10002470 . C T 30.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:26:42:0,42:1:30,28,0
chr20 10002493 . A C 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:59:37:32,5:0.135135:0,61,61
chr20 10002625 . G T 55.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:51:55:0,55:1:55,52,0
chr20 10003021 . C T 49.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:44:38:0,38:1:49,45,0
chr20 10003109 . A C 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:55:32:28,4:0.125:0,55,62
chr20 10003358 . A C 46.4 PASS . GT:GQ:DP:AD:VAF:PL 0/1:46:51:24,27:0.529412:46,0,58
chr20 10003651 . T C 52.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:46:44:0,44:1:52,46,0
chr20 10003692 . A G 56.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:51:44:0,44:1:56,51,0
chr20 10003832 . G A 54 PASS . GT:GQ:DP:AD:VAF:PL 1/1:47:37:0,37:1:54,47,0
chr20 10004094 . A C 56 PASS . GT:GQ:DP:AD:VAF:PL 1/1:50:35:0,35:1:55,51,0
chr20 10004147 . A G 56.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:50:41:0,41:1:56,50,0
chr20 10004193 . G T 47.9 PASS . GT:GQ:DP:AD:VAF:PL 0/1:45:42:19,21:0.5:47,0,47
chr20 10004222 . C CA 27.4 PASS . GT:GQ:DP:AD:VAF:PL 0/1:24:50:20,28:0.56:27,0,26
chr20 10004223 . A AG 20.4 PASS . GT:GQ:DP:AD:VAF:PL 0/1:20:54:39,15:0.277778:20,0,38
chr20 10004253 . A T 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:49:55:48,7:0.127273:0,50,56
chr20 10004351 . C G 58.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:55:50:0,50:1:58,58,0
chr20 10004389 . T G 45.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:40:41:0,41:1:45,41,0
chr20 10004610 . A C 49.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:46:51:0,51:1:49,49,0
chr20 10004725 . A G 27.3 PASS . GT:GQ:DP:AD:VAF:PL 0/1:26:51:27,24:0.470588:27,0,31
chr20 10004769 . TAAAACTATGC T 38.9 PASS . GT:GQ:DP:AD:VAF:PL 0/1:37:53:14,39:0.735849:38,0,40
chr20 10004874 . A C 46.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:41:58:0,58:1:46,41,0
chr20 10004887 . A G 39.8 PASS . GT:GQ:DP:AD:VAF:PL 0/1:39:57:30,27:0.473684:39,0,47
chr20 10005010 . C T 51.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:47:54:0,54:1:51,48,0
chr20 10005427 . C T 55.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:44:0,44:1:55,49,0
chr20 10005499 . A G 54 PASS . GT:GQ:DP:AD:VAF:PL 1/1:51:45:0,45:1:54,53,0
chr20 10005587 . A G 48.9 PASS . GT:GQ:DP:AD:VAF:PL 0/1:48:61:31,30:0.491803:48,0,56
chr20 10005723 . A G 55.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:50:53:0,53:1:55,51,0
chr20 10006291 . G A 32.7 PASS . GT:GQ:DP:AD:VAF:PL 0/1:33:55:29,26:0.472727:32,0,48
chr20 10006404 . A C 57 PASS . GT:GQ:DP:AD:VAF:PL 1/1:53:50:0,50:1:57,54,0
chr20 10006682 . T A 45.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:42:47:0,47:1:45,43,0
chr20 10006819 . AAAAC A 50.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:46:44:0,44:1:50,48,0
chr20 10007150 . G C 50.2 PASS . GT:GQ:DP:AD:VAF:PL 0/1:50:46:29,17:0.369565:50,0,67
chr20 10007175 . C T 38.8 PASS . GT:GQ:DP:AD:VAF:PL 0/1:39:45:22,23:0.511111:38,0,51
chr20 10007352 . C T 50.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:44:45:0,45:1:50,45,0
chr20 10007531 . A G 51.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:45:51:0,51:1:51,45,0
chr20 10007980 . A C 51.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:45:61:0,61:1:51,45,0
chr20 10008029 . T TA 50.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:38:43:0,43:1:50,38,0
chr20 10008146 . TA T 47.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:42:46:0,46:1:47,43,0
chr20 10008221 . T C 53.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:49:51:0,51:1:53,50,0
chr20 10008458 . T G 46 PASS . GT:GQ:DP:AD:VAF:PL 1/1:41:36:0,36:1:46,43,0
chr20 10008717 . AT A 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:54:25:23,2:0.08:0,53,65
chr20 10008742 . G T 31.6 PASS . GT:GQ:DP:AD:VAF:PL 0/1:23:31:13,16:0.516129:31,0,24
chr20 10008750 . T TAA 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:40:27:21,2:0.0740741:0,39,52
chr20 10008758 . C CA 29.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:21:31:4,19:0.612903:29,21,0
chr20 10008921 . C CA 28.1 PASS . GT:GQ:DP:AD:VAF:PL 0/1:28:29:17,8:0.275862:28,0,53
chr20 10008948 . TA T 42.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:33:40:0,40:1:42,33,0
chr20 10008952 . CACACACACACA C,CCACACACACA 36.7 PASS . GT:GQ:DP:AD:VAF:PL 1/2:15:42:2,14,25:0.333333,0.595238:36,24,37,24,0,15
chr20 10009227 . A G 51.4 PASS . GT:GQ:DP:AD:VAF:PL 0/1:50:66:34,32:0.484848:51,0,55
chr20 10009246 . A G 49.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:68:0,68:1:49,52,0
chr20 10009400 . T A 36.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:35:70:0,70:1:36,41,0
chr20 10009512 . C G 48.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:44:47:0,47:1:48,46,0
chr20 10009719 . A G 53.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:50:33:0,33:1:53,52,0
chr20 10009795 . A G 46.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:45:40:0,40:1:46,50,0
chr20 10009844 . G A,AAGAGAGAG 24.8 PASS . GT:GQ:DP:AD:VAF:PL 1/2:3:41:6,30,5:0.731707,0.121951:21,15,0,15,0,9
chr20 10009871 . A G 22.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:18:47:5,42:0.893617:22,19,0
chr20 10009875 . A G 22.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:20:51:5,46:0.901961:22,24,0
chr20 10009879 . A G 20 PASS . GT:GQ:DP:AD:VAF:PL 1/1:19:48:0,48:1:19,25,0
chr20 10009883 . A G 31.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:30:50:0,50:1:31,37,0
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18 changes: 9 additions & 9 deletions deepvariant/testdata/golden.training_examples.tfrecord.gz.run_info.pbtxt
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Expand Up @@ -3409,7 +3409,7 @@ options {
allele_counter_options {
partition_size: 1000
read_requirements {
min_mapping_quality: 10
min_mapping_quality: 5
min_base_quality: 10
min_base_quality_mode: ENFORCED_BY_CLIENT
}
Expand Down Expand Up @@ -3445,7 +3445,7 @@ options {
base_quality_cap: 40
read_overlap_buffer_bp: 5
read_requirements {
min_mapping_quality: 10
min_mapping_quality: 5
min_base_quality: 10
min_base_quality_mode: ENFORCED_BY_CLIENT
}
Expand All @@ -3457,7 +3457,7 @@ options {
other_allele_supporting_read_alpha: 0.6000000238418579
}
read_requirements {
min_mapping_quality: 10
min_mapping_quality: 5
min_base_quality: 10
min_base_quality_mode: ENFORCED_BY_CLIENT
}
Expand Down Expand Up @@ -3531,12 +3531,12 @@ labeling_metrics {
resource_metrics {
host_name: "host"
physical_core_count: 6
cpu_frequency_mhz: 1240.7578333333333
cpu_frequency_mhz: 1301.7215833333332
total_memory_mb: 64142
wall_time_seconds: 0.9516043663024902
cpu_user_time_seconds: 5.506375
cpu_system_time_seconds: 0.8286089999999999
memory_peak_rss_mb: 375
read_bytes: 294600704
wall_time_seconds: 1.6400227546691895
cpu_user_time_seconds: 8.997739
cpu_system_time_seconds: 4.470188
memory_peak_rss_mb: 371
read_bytes: 802750464
write_bytes: 20480
}
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