depth of indel in a uncalled snp site
Hello,
There is an indel called by HaplotypeCaller with a high allel depth(61), but in IGV the count of indel is 12 . The location has C alell but it is uncalled. I checked near sites and there is no variant called. Can we clarify the issue?
Thank you
VCF:
chr17 80090216 . G GGGACGCGCGCAGGCACGTGCACGAAC 1499.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.066;DP=138;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.69;MQRankSum=-8.760;QD=11.11;ReadPosRankSum=-5.013;SOR=0.547;set=variant2 GT:AD:DP:GQ:PL ./. 0/1:74,61:135:99:1507,0,2139
a) GATK version used: 4.3.0.0
b) Exact command used: gatk-4.3.0.0/gatk --java-options "-Xmx160G -XX:ParallelGCThreads=44" HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I recal_reads_S16.bam -L wes.bed -bamout hc_S16.bam -ip 20 -O raw_variants_S16.vcf
c) Entire program log: Using GATK jar gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx160G -XX:ParallelGCThreads=44 -jar gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I recal_reads_S16.bam -L wes.bed -bamout hc_S16.bam -ip 20 -O raw_variants_S16.vcf
19:10:10.695 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file: gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
19:10:10.975 INFO HaplotypeCaller - ------------------------------------------------------------
19:10:10.975 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.3.0.0
19:10:10.975 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
19:10:10.975 INFO HaplotypeCaller - Executing as sselvi@server013.mesten.local on Linux v3.10.0-1062.12.1.el7.x86_64 amd64
19:10:10.975 INFO HaplotypeCaller - Java runtime: IBM J9 VM v8.0.5.30 - pxa6480sr5fp30-20190207_01(SR5 FP30)
19:10:10.976 INFO HaplotypeCaller - Start Date/Time: August 11, 2023 7:10:10 PM TRT
19:10:10.976 INFO HaplotypeCaller - ------------------------------------------------------------
19:10:10.976 INFO HaplotypeCaller - ------------------------------------------------------------
19:10:10.976 INFO HaplotypeCaller - HTSJDK Version: 3.0.1
19:10:10.976 INFO HaplotypeCaller - Picard Version: 2.27.5
19:10:10.976 INFO HaplotypeCaller - Built for Spark Version: 2.4.5
19:10:10.976 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:10:10.976 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:10:10.976 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:10:10.977 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:10:10.977 INFO HaplotypeCaller - Deflater: IntelDeflater
19:10:10.977 INFO HaplotypeCaller - Inflater: IntelInflater
19:10:10.977 INFO HaplotypeCaller - GCS max retries/reopens: 20
19:10:10.977 INFO HaplotypeCaller - Requester pays: disabled
19:10:10.977 INFO HaplotypeCaller - Initializing engine
19:10:11.924 INFO FeatureManager - Using codec BEDCodec to read file file://wes.bed
19:10:12.628 INFO IntervalArgumentCollection - Processing 41625045 bp from intervals
19:10:12.998 INFO HaplotypeCaller - Done initializing engine
19:10:13.163 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
19:10:13.303 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
19:10:13.304 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
19:10:13.336 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
19:10:13.336 INFO IntelPairHmm - Available threads: 44
19:10:13.336 INFO IntelPairHmm - Requested threads: 4
19:10:13.336 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
19:10:13.474 INFO ProgressMeter - Starting traversal
19:10:13.474 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
19:10:14.531 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position chr1:69270 and possibly subsequent; at least 10 samples must have called genotypes
19:10:23.594 INFO ProgressMeter - chr1:1291415 0.2 280 1660.1
19:10:33.662 INFO ProgressMeter - chr1:2519121 0.3 820 2437.1
19:10:43.785 INFO ProgressMeter - chr1:6473296 0.5 1350 2672.3
19:10:53.823 INFO ProgressMeter - chr1:11037671 0.7 1970 2929.4
19:11:03.923 INFO ProgressMeter - chr1:15562120 0.8 2740 3258.8
19:11:14.138 INFO ProgressMeter - chr1:17348005 1.0 3280 3244.1
19:11:24.226 INFO ProgressMeter - chr1:21597698 1.2 3920 3324.3
19:11:34.291 INFO ProgressMeter - chr1:24840751 1.3 4610 3422.5
19:11:44.347 INFO ProgressMeter - chr1:28496512 1.5 5340 3525.8
19:11:54.661 INFO ProgressMeter - chr1:33488443 1.7 6100 3617.1
19:12:04.668 INFO ProgressMeter - chr1:37835057 1.9 6800 3669.3
19:12:14.773 INFO ProgressMeter - chr1:42456844 2.0 7480 3699.9
19:12:24.781 INFO ProgressMeter - chr1:45508219 2.2 8250 3769.8
19:12:35.036 INFO ProgressMeter - chr1:53093439 2.4 9150 3878.2
19:12:45.112 INFO ProgressMeter - chr1:61914565 2.5 9850 3897.4
19:12:55.191 INFO ProgressMeter - chr1:70852817 2.7 10580 3925.4
19:13:05.266 INFO ProgressMeter - chr1:86485321 2.9 11400 3981.6
19:13:15.379 INFO ProgressMeter - chr1:94174229 3.0 12140 4004.3
19:13:25.681 INFO ProgressMeter - chr1:109252742 3.2 13030 4067.5
19:13:35.724 INFO ProgressMeter - chr1:112713475 3.4 13710 4067.3
19:13:45.727 INFO ProgressMeter - chr1:145391508 3.5 14710 4158.2
19:13:55.734 INFO ProgressMeter - chr1:151002143 3.7 15680 4232.9
19:14:06.082 INFO ProgressMeter - chr1:152304730 3.9 16190 4176.1
19:14:16.777 INFO ProgressMeter - chr1:152312586 4.1 16250 4007.3
19:14:27.524 INFO ProgressMeter - chr1:154869674 4.2 16910 3993.7
19:14:37.612 INFO ProgressMeter - chr1:156592389 4.4 17710 4022.9
19:14:47.700 INFO ProgressMeter - chr1:158661265 4.6 18280 3999.6
19:14:57.761 INFO ProgressMeter - chr1:161209171 4.7 18950 3999.5
19:15:07.868 INFO ProgressMeter - chr1:169707320 4.9 19700 4015.0
19:15:17.983 INFO ProgressMeter - chr1:176888174 5.1 20370 4013.7
19:15:28.184 INFO ProgressMeter - chr1:183125375 5.2 21050 4013.2
19:15:38.247 INFO ProgressMeter - chr1:197652213 5.4 21930 4051.4
19:15:48.318 INFO ProgressMeter - chr1:202736191 5.6 22600 4049.6
19:15:58.912 INFO ProgressMeter - chr1:205845319 5.8 23220 4033.2
19:16:08.961 INFO ProgressMeter - chr1:212887869 5.9 24020 4054.2
19:16:19.045 INFO ProgressMeter - chr1:222523590 6.1 24580 4034.2
19:16:29.139 INFO ProgressMeter - chr1:227734990 6.3 25180 4021.7
19:16:39.148 INFO ProgressMeter - chr1:230325296 6.4 25640 3988.9
19:16:49.231 INFO ProgressMeter - chr1:236547990 6.6 26280 3984.3
19:16:59.265 INFO ProgressMeter - chr1:247423825 6.8 27070 4002.6
19:17:10.094 INFO ProgressMeter - chr1:248361761 6.9 27270 3927.3
19:17:20.305 INFO ProgressMeter - chr2:3189312 7.1 27550 3872.7
19:17:30.727 INFO ProgressMeter - chr2:18555769 7.3 28340 3888.8
19:17:40.765 INFO ProgressMeter - chr2:26898478 7.5 29120 3906.2
19:17:50.898 INFO ProgressMeter - chr2:30787149 7.6 29920 3924.6
19:18:00.917 INFO ProgressMeter - chr2:42708852 7.8 30830 3957.3
19:18:11.054 INFO ProgressMeter - chr2:54255865 8.0 31570 3966.2
19:18:21.119 INFO ProgressMeter - chr2:68188598 8.1 32450 3992.7
19:18:31.214 INFO ProgressMeter - chr2:73813455 8.3 33190 4000.9
19:18:41.338 INFO ProgressMeter - chr2:86105724 8.5 34010 4018.0
19:18:51.374 INFO ProgressMeter - chr2:97792921 8.6 34930 4046.7
19:19:01.396 INFO ProgressMeter - chr2:107988134 8.8 35710 4058.6
19:19:11.484 INFO ProgressMeter - chr2:119311656 9.0 36630 4085.1
19:19:21.533 INFO ProgressMeter - chr2:130370683 9.1 37300 4083.5
19:19:31.544 INFO ProgressMeter - chr2:141229161 9.3 37940 4079.1
19:19:41.588 INFO ProgressMeter - chr2:159852179 9.5 38850 4103.0
19:19:52.306 INFO ProgressMeter - chr2:169243430 9.6 39700 4115.2
19:20:02.676 INFO ProgressMeter - chr2:177617053 9.8 40500 4124.2
19:20:12.719 INFO ProgressMeter - chr2:179146380 10.0 41360 4141.2
19:20:22.857 INFO ProgressMeter - chr2:189666411 10.2 42030 4138.3
19:20:32.871 INFO ProgressMeter - chr2:200817084 10.3 42820 4147.9
19:20:42.960 INFO ProgressMeter - chr2:208325756 10.5 43740 4169.1
19:20:53.057 INFO ProgressMeter - chr2:218430703 10.7 44490 4173.7
19:21:03.259 INFO ProgressMeter - chr2:219541963 10.8 45110 4165.4
19:21:13.294 INFO ProgressMeter - chr2:230049739 11.0 45810 4165.7
19:21:23.654 INFO ProgressMeter - chr2:233713570 11.2 46510 4164.0
19:21:33.754 INFO ProgressMeter - chr2:240462469 11.3 47130 4156.8
19:21:43.924 INFO ProgressMeter - chr3:3040015 11.5 47670 4142.5
19:21:53.965 INFO ProgressMeter - chr3:10918307 11.7 48360 4142.2
19:22:03.967 INFO ProgressMeter - chr3:23589712 11.8 49180 4153.2
19:22:14.027 INFO ProgressMeter - chr3:38365245 12.0 50070 4169.3
19:22:24.253 INFO ProgressMeter - chr3:43055410 12.2 50710 4163.5
19:22:34.255 INFO ProgressMeter - chr3:47003794 12.3 51360 4159.9
19:22:44.295 INFO ProgressMeter - chr3:49111889 12.5 52180 4169.8
19:22:54.309 INFO ProgressMeter - chr3:51393104 12.7 53000 4179.6
19:23:04.436 INFO ProgressMeter - chr3:53857594 12.8 53880 4193.2
19:23:14.465 INFO ProgressMeter - chr3:69038542 13.0 54740 4205.4
19:23:24.742 INFO ProgressMeter - chr3:75737859 13.2 54990 4169.8
19:23:34.826 INFO ProgressMeter - chr3:98149735 13.4 55300 4140.5
19:23:44.892 INFO ProgressMeter - chr3:111072398 13.5 56030 4143.1
19:23:55.302 INFO ProgressMeter - chr3:119416245 13.7 56680 4138.1
19:24:05.447 INFO ProgressMeter - chr3:123739009 13.9 57400 4139.6
19:24:15.527 INFO ProgressMeter - chr3:129567676 14.0 58180 4145.6
19:24:25.750 INFO ProgressMeter - chr3:138167059 14.2 58920 4148.0
19:24:35.953 INFO ProgressMeter - chr3:150411245 14.4 59740 4155.9
19:24:46.040 INFO ProgressMeter - chr3:169127914 14.5 60610 4167.7
19:24:56.041 INFO ProgressMeter - chr3:183206100 14.7 61320 4168.7
19:25:06.051 INFO ProgressMeter - chr3:187250229 14.9 62130 4176.4
19:25:16.449 INFO ProgressMeter - chr3:195747251 15.0 62610 4160.2
19:25:30.770 INFO ProgressMeter - chr3:195786424 15.3 62700 4101.2
19:25:40.784 INFO ProgressMeter - chr4:1000627 15.5 63310 4096.4
19:25:50.800 INFO ProgressMeter - chr4:3178332 15.6 63830 4085.9
19:26:01.449 INFO ProgressMeter - chr4:8227949 15.8 64410 4076.7
19:26:11.505 INFO ProgressMeter - chr4:20567240 16.0 65100 4077.1
19:26:21.544 INFO ProgressMeter - chr4:40335854 16.1 65870 4082.6
19:26:31.548 INFO ProgressMeter - chr4:54727394 16.3 66650 4088.6
19:26:41.562 INFO ProgressMeter - chr4:70409958 16.5 67420 4094.0
19:26:51.753 INFO ProgressMeter - chr4:78472158 16.6 68230 4100.9
19:27:01.832 INFO ProgressMeter - chr4:88851113 16.8 69100 4111.6
19:27:11.939 INFO ProgressMeter - chr4:106116332 17.0 69870 4116.2
19:27:21.996 INFO ProgressMeter - chr4:119520913 17.1 70610 4119.1
19:27:32.363 INFO ProgressMeter - chr4:139889584 17.3 71340 4120.2
19:27:42.375 INFO ProgressMeter - chr4:153295896 17.5 72070 4122.6
19:27:52.536 INFO ProgressMeter - chr4:168511728 17.7 72820 4125.5
19:28:02.589 INFO ProgressMeter - chr4:186157594 17.8 73580 4129.4
19:28:12.602 INFO ProgressMeter - chr5:1414669 18.0 74130 4121.7
19:28:22.647 INFO ProgressMeter - chr5:14292990 18.2 74680 4113.9
19:28:32.652 INFO ProgressMeter - chr5:36211822 18.3 75480 4120.2
19:28:43.080 INFO ProgressMeter - chr5:54543157 18.5 76390 4130.7
19:28:53.265 INFO ProgressMeter - chr5:69365521 18.7 77270 4140.2
19:29:03.337 INFO ProgressMeter - chr5:77693269 18.8 78100 4147.4
19:29:13.557 INFO ProgressMeter - chr5:90828922 19.0 78840 4149.2
19:29:23.618 INFO ProgressMeter - chr5:112842112 19.2 79670 4156.2
19:29:33.693 INFO ProgressMeter - chr5:127369888 19.3 80300 4152.7
19:29:43.742 INFO ProgressMeter - chr5:136052885 19.5 81120 4159.0
19:29:53.790 INFO ProgressMeter - chr5:140803154 19.7 81870 4161.8
19:30:03.992 INFO ProgressMeter - chr5:141174038 19.8 82090 4137.2
19:30:14.069 INFO ProgressMeter - chr5:141526016 20.0 82420 4119.0
19:30:24.069 INFO ProgressMeter - chr5:150050230 20.2 83220 4124.6
19:30:34.323 INFO ProgressMeter - chr5:154297919 20.3 83750 4116.0
19:30:44.470 INFO ProgressMeter - chr5:169596539 20.5 84480 4117.6
19:30:54.539 INFO ProgressMeter - chr5:177366869 20.7 85240 4121.0
19:31:04.599 INFO ProgressMeter - chr5:180318771 20.9 85840 4116.6
19:31:14.631 INFO ProgressMeter - chr6:7309895 21.0 86420 4111.5
19:31:24.662 INFO ProgressMeter - chr6:24418596 21.2 87210 4116.3
19:31:34.887 INFO ProgressMeter - chr6:29174238 21.4 87930 4117.2
19:31:45.124 INFO ProgressMeter - chr6:30647864 21.5 88280 4100.8
19:31:55.335 INFO ProgressMeter - chr6:31157518 21.7 88640 4085.2
19:32:05.469 INFO ProgressMeter - chr6:31829586 21.9 89060 4072.9
19:32:17.306 INFO ProgressMeter - chr6:32584155 22.1 89590 4060.5
19:32:27.425 INFO ProgressMeter - chr6:32937242 22.2 89700 4034.6
19:32:37.432 INFO ProgressMeter - chr6:34035646 22.4 90180 4026.0
19:32:47.553 INFO ProgressMeter - chr6:36954946 22.6 90720 4019.9
19:32:57.566 INFO ProgressMeter - chr6:42652001 22.7 91420 4021.1
19:33:07.681 INFO ProgressMeter - chr6:46143254 22.9 92180 4024.7
19:33:17.823 INFO ProgressMeter - chr6:54124691 23.1 92840 4023.8
19:33:28.031 INFO ProgressMeter - chr6:73225275 23.2 93590 4026.7
19:33:38.043 INFO ProgressMeter - chr6:88614250 23.4 94520 4037.7
19:33:48.302 INFO ProgressMeter - chr6:107070563 23.6 95300 4041.5
19:33:58.404 INFO ProgressMeter - chr6:116279095 23.7 95970 4041.0
19:34:08.404 INFO ProgressMeter - chr6:131573261 23.9 96810 4048.0
19:34:18.606 INFO ProgressMeter - chr6:142770164 24.1 97570 4051.0
19:34:28.631 INFO ProgressMeter - chr6:151880703 24.3 98240 4050.7
19:34:38.908 INFO ProgressMeter - chr6:159238532 24.4 98920 4050.1
19:34:48.938 INFO ProgressMeter - chr6:168057075 24.6 99540 4047.8
19:34:58.996 INFO ProgressMeter - chr7:2278078 24.8 100060 4041.4
19:35:09.002 INFO ProgressMeter - chr7:6584994 24.9 100730 4041.2
19:35:19.077 INFO ProgressMeter - chr7:21617597 25.1 101430 4042.1
19:35:29.084 INFO ProgressMeter - chr7:30655558 25.3 102110 4042.3
19:35:39.158 INFO ProgressMeter - chr7:43876645 25.4 102870 4045.5
19:35:49.515 INFO ProgressMeter - chr7:51029329 25.6 103640 4048.3
19:35:59.609 INFO ProgressMeter - chr7:74061079 25.8 104380 4050.6
19:36:11.032 INFO ProgressMeter - chr7:83385272 26.0 105200 4052.5
19:36:21.353 INFO ProgressMeter - chr7:94412046 26.1 105950 4054.5
19:36:31.483 INFO ProgressMeter - chr7:100374174 26.3 106810 4061.2
19:36:42.471 INFO ProgressMeter - chr7:100952670 26.5 107200 4047.8
19:36:53.311 INFO ProgressMeter - chr7:100956183 26.7 107220 4021.2
19:37:05.678 INFO ProgressMeter - chr7:100960730 26.9 107250 3991.4
19:37:15.761 INFO ProgressMeter - chr7:102278056 27.0 107580 3978.8
19:37:25.814 INFO ProgressMeter - chr7:111782842 27.2 108450 3986.3
19:37:35.982 INFO ProgressMeter - chr7:128352421 27.4 109250 3990.8
19:37:46.054 INFO ProgressMeter - chr7:135584810 27.5 110020 3994.5
19:37:56.247 INFO ProgressMeter - chr7:142750533 27.7 110800 3998.1
19:38:06.356 INFO ProgressMeter - chr7:144362948 27.9 111170 3987.3
19:38:16.685 INFO ProgressMeter - chr7:151200361 28.1 111800 3985.2
19:38:26.923 INFO ProgressMeter - chr7:158886999 28.2 112380 3981.7
19:38:37.578 INFO ProgressMeter - chr8:10610213 28.4 113010 3979.0
19:38:47.704 INFO ProgressMeter - chr8:18808733 28.6 113570 3975.1
19:38:57.720 INFO ProgressMeter - chr8:25345544 28.7 114300 3977.4
19:39:07.883 INFO ProgressMeter - chr8:33512389 28.9 115010 3978.6
19:39:17.897 INFO ProgressMeter - chr8:50658575 29.1 115960 3988.5
19:39:28.013 INFO ProgressMeter - chr8:68096996 29.2 116780 3993.5
19:39:38.050 INFO ProgressMeter - chr8:94148788 29.4 117750 4003.8
19:39:48.081 INFO ProgressMeter - chr8:104499480 29.6 118590 4009.6
19:39:58.081 INFO ProgressMeter - chr8:123799750 29.7 119410 4014.7
19:40:08.178 INFO ProgressMeter - chr8:141190331 29.9 120190 4018.2
19:40:18.513 INFO ProgressMeter - chr8:143606445 30.1 120530 4006.5
19:40:28.588 INFO ProgressMeter - chr8:144058751 30.3 120940 3997.8
19:40:39.525 INFO ProgressMeter - chr9:117840 30.4 121570 3994.5
19:40:49.580 INFO ProgressMeter - chr9:8341971 30.6 122150 3991.6
19:40:59.751 INFO ProgressMeter - chr9:27205061 30.8 122920 3994.6
19:41:09.885 INFO ProgressMeter - chr9:35093008 30.9 123550 3993.2
19:41:19.998 INFO ProgressMeter - chr9:41127856 31.1 124260 3994.4
19:41:30.098 INFO ProgressMeter - chr9:76323030 31.3 125040 3997.8
19:41:40.605 INFO ProgressMeter - chr9:87888499 31.5 125730 3997.5
19:41:50.683 INFO ProgressMeter - chr9:97320104 31.6 126500 4000.6
19:42:00.710 INFO ProgressMeter - chr9:104752896 31.8 127090 3998.1
19:42:10.734 INFO ProgressMeter - chr9:113196910 32.0 127890 4002.3
19:42:20.775 INFO ProgressMeter - chr9:120821333 32.1 128470 3999.5
19:42:30.787 INFO ProgressMeter - chr9:125002064 32.3 129090 3998.0
19:42:40.987 INFO ProgressMeter - chr9:128791358 32.5 129930 4003.0
19:42:51.014 INFO ProgressMeter - chr9:132014315 32.6 130620 4003.6
19:43:01.089 INFO ProgressMeter - chr9:134728648 32.8 131210 4001.1
19:43:11.185 INFO ProgressMeter - chr9:136476853 33.0 131730 3996.4
19:43:21.200 INFO ProgressMeter - chr9:137267218 33.1 132330 3994.4
19:43:31.266 INFO ProgressMeter - chr10:5894468 33.3 132990 3994.1
19:43:41.312 INFO ProgressMeter - chr10:17115449 33.5 133760 3997.1
19:43:51.351 INFO ProgressMeter - chr10:27060490 33.6 134490 3999.0
19:44:01.364 INFO ProgressMeter - chr10:37149755 33.8 135060 3996.1
19:44:11.848 INFO ProgressMeter - chr10:46579147 34.0 135490 3988.2
19:44:21.916 INFO ProgressMeter - chr10:59654591 34.1 136240 3990.5
19:44:31.969 INFO ProgressMeter - chr10:69940966 34.3 136980 3992.6
19:44:42.061 INFO ProgressMeter - chr10:75398727 34.5 137810 3997.2
19:44:52.083 INFO ProgressMeter - chr10:88910894 34.6 138530 3998.7
19:45:02.140 INFO ProgressMeter - chr10:96156601 34.8 139400 4004.5
19:45:12.147 INFO ProgressMeter - chr10:100194403 35.0 140090 4005.1
19:45:22.265 INFO ProgressMeter - chr10:103602310 35.1 140890 4008.6
19:45:32.341 INFO ProgressMeter - chr10:114333199 35.3 141680 4012.0
19:45:42.365 INFO ProgressMeter - chr10:123768504 35.5 142560 4017.9
19:45:52.454 INFO ProgressMeter - chr10:132690370 35.6 143150 4015.5
19:46:02.509 INFO ProgressMeter - chr11:400638 35.8 143630 4010.1
19:46:20.539 INFO ProgressMeter - chr11:1017292 36.1 144070 3988.9
19:46:30.591 INFO ProgressMeter - chr11:1020068 36.3 144080 3970.8
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20:18:33.755 INFO HaplotypeCaller - 1769544 read(s) filtered by: MappingQualityReadFilter
0 read(s) filtered by: MappingQualityAvailableReadFilter
0 read(s) filtered by: MappedReadFilter
544686 read(s) filtered by: NotSecondaryAlignmentReadFilter
3781676 read(s) filtered by: NotDuplicateReadFilter
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0 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
6095906 total reads filtered
20:18:33.756 INFO ProgressMeter - chrY:57191776 68.3 270325 3955.7
20:18:33.756 INFO ProgressMeter - Traversal complete. Processed 270325 total regions in 68.3 minutes.
20:18:34.024 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 3.210550726
20:18:34.024 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 331.3094062
20:18:34.024 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 944.64 sec
20:18:50.747 INFO HaplotypeCaller - Shutting down engine
[August 11, 2023 8:18:50 PM TRT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 68.67 minutes.
Runtime.totalMemory()=2019622912
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Hi Sinem Selvi
HaplotypeCaller uses local reassembly of reads using debruijin graphs and PairHMM to generate its calls in detected active regions of your alignment files. Due to this behavior what you observe in IGV as the pileup of reads may not fully represent what HaplotypeCaller sees and genotypes in that region. If you wish to check what HaplotypeCaller generates as assembly in that region you may use the
--bam-output bamout.bam
option to generate a bam file of genotyped haplotypes of the active region and you may compare that to the original alignment file in IGV. From the command line that you posted you seem to have used this option already. You may check the hc_S16.bam file with IGV to see the actual calls.
Looking at your issue here we have a few suggestions for you to try before you decide the best option for your calls.
- Interval padding you use for your bed file is 20 basepairs which may be a little too low for our recommendation. We have seen by multiple user feedbacks and our own internal testing that haplotypecaller may generate slightly different calls due to reference intervals provided for the walker. As more or less reference is provided, different number of reads are available for the tool to generate and realign to the provided reference therefore graph construction and genotyping may slightly change due to this behavior. This may result in certain calls to be unexpected or missing. To change this behavior you may decide to remove bed file usage completely which gives the tool ultimate collection of reads to process and realign to the whole active region freely (recommended option) resulting in less false negatives and better assemblies or if you still have to use it increase interval padding to at least 150 to 250 basepairs to provide more room to recover and assemble haplotypes
- Certain experimental options of HaplotypeCaller may provide more refined assemblies and less false negatives but these options are still beta such as
--linked-de-bruijn-graph true
More information can be found in the following article
If you still observe an issue you may share a slice of your bam file including up to 1000 BPs upstream and downstream of the region of interest and upload it according to the instructions given below and we may try to replicate your issue.
https://gatk.broadinstitute.org/hc/en-us/articles/360035889671
I hope this helps.
PS: The region you are checking in this instance is a quite variable region with lots of INDELs and SNPs with mostly low qual scores. A very GC rich region and you may observe lots of bad assemblies with short reads in there so be careful.
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1- represented bam file is output of HaplotypeCaller.
2-Actually before solving the problem, I would like to know what caused the issue of not matching variant informations on hc bam and vcf file?
Thank you
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Hi Sinem Selvi
The answer lies with uninformative reads in the assembly/bamout and actual bam file.
In terms of local assembly not all reads are equal to HaplotypeCaller therefore some get filtered out in the calculation steps however this does not mean they are not used by local assembly or the bamout file.
As we mentioned before local reassembly can be more complicated that it looks especially when there are repetitive regions of GC rich complex regions. In that case some of the reads although they seem to be supporting a variant they are eliminated by HaplotypeCaller and local assembly filters.
If you still think that you cannot call a known variant you can send us a snippet of the bam file and we may check those reasons in more detail.
Regards.
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