I'm trying to run gatk4 HaplotypeCaller using the following command:
./gatk HaplotypeCaller -R ./reference.fasta --emit-ref-confidence GVCF --dbsnp ./samtools_gatk_common.vcf -I ./sample.bqsr.bam -O ./sample.gvcf --TMP_DIR ./tmp
the log output gives no error but the result *.gvcf file only contained header and one base recode. The dbsnp file was the intersection of samtools and gatk.
here the log file:
Using GATK jar /path/to/gatk-4.0.4.0/gatk-package-4.0.4.0-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 -jar /path/to/gatk-4.0.4.0/gatk-package-4.0.4.0-local.jar HaplotypeCaller -R /path/to/index/chrom23.fasta --emit-ref-confidence GVCF --dbsnp /path/to/dbsnp/sample.dbsnp.vcf -I /path/to/BQSR/sample.bqsr.bam -O /path/to/result/sample.g.vcf --TMP_DIR /path/to/tmp
18:38:47.051 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/path/to/gatk-4.0.4.0/gatk-package-4.0.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
18:38:47.439 INFO HaplotypeCaller - ------------------------------------------------------------
18:38:47.440 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.0.4.0
18:38:47.440 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
18:38:47.442 INFO HaplotypeCaller - Executing as hankai@cngb-compute-e05-6.cngb.sz.hpc on Linux v2.6.32-696.el6.x86_64 amd64
18:38:47.442 INFO HaplotypeCaller - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_172-b11
18:38:47.442 INFO HaplotypeCaller - Start Date/Time: July 4, 2018 6:38:46 PM CST
18:38:47.442 INFO HaplotypeCaller - ------------------------------------------------------------
18:38:47.442 INFO HaplotypeCaller - ------------------------------------------------------------
18:38:47.443 INFO HaplotypeCaller - HTSJDK Version: 2.14.3
18:38:47.443 INFO HaplotypeCaller - Picard Version: 2.18.2
18:38:47.444 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:38:47.444 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:38:47.444 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:38:47.444 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:38:47.444 INFO HaplotypeCaller - Deflater: IntelDeflater
18:38:47.444 INFO HaplotypeCaller - Inflater: IntelInflater
18:38:47.444 INFO HaplotypeCaller - GCS max retries/reopens: 20
18:38:47.444 INFO HaplotypeCaller - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
18:38:47.444 INFO HaplotypeCaller - Initializing engine
18:38:50.210 INFO FeatureManager - Using codec VCFCodec to read file file:///path/to/dbsnp/sample.dbsnp.vcf
18:38:50.292 INFO HaplotypeCaller - Done initializing engine
18:38:50.303 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
18:38:50.303 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output
18:38:51.794 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/path/to/gatk-4.0.4.0/gatk-package-4.0.4.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
18:38:51.817 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/path/to/gatk-4.0.4.0/gatk-package-4.0.4.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
18:38:51.915 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
18:38:51.916 INFO IntelPairHmm - Available threads: 112
18:38:51.916 INFO IntelPairHmm - Requested threads: 4
18:38:51.916 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
18:38:51.996 INFO ProgressMeter - Starting traversal
18:38:51.997 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
18:39:02.152 INFO ProgressMeter - pseudochrom_23:39888 0.2 240 1418.4
18:39:12.324 INFO ProgressMeter - pseudochrom_23:112351 0.3 650 1918.6
18:39:22.383 INFO ProgressMeter - pseudochrom_23:166271 0.5 980 1935.1
18:39:32.471 INFO ProgressMeter - pseudochrom_23:208604 0.7 1240 1838.3
18:39:42.498 INFO ProgressMeter - pseudochrom_23:270983 0.8 1610 1912.8
18:39:52.827 INFO ProgressMeter - pseudochrom_23:315473 1.0 1890 1864.2
18:40:03.130 INFO ProgressMeter - pseudochrom_23:368748 1.2 2220 1872.5
18:40:13.602 INFO ProgressMeter - pseudochrom_23:430805 1.4 2590 1905.3
18:40:23.620 INFO ProgressMeter - pseudochrom_23:512763 1.5 3060 2003.9
18:40:33.781 INFO ProgressMeter - pseudochrom_23:592148 1.7 3540 2086.8
18:40:46.199 INFO ProgressMeter - pseudochrom_23:661025 1.9 3950 2075.3
18:40:56.336 INFO ProgressMeter - pseudochrom_23:731629 2.1 4380 2113.6
18:41:09.819 INFO ProgressMeter - pseudochrom_23:835707 2.3 5000 2176.7
18:41:19.874 INFO ProgressMeter - pseudochrom_23:941548 2.5 5630 2284.3
18:41:30.479 INFO ProgressMeter - pseudochrom_23:1044902 2.6 6230 2358.6
18:41:40.552 INFO ProgressMeter - pseudochrom_23:1157010 2.8 6910 2459.7
18:41:50.606 INFO ProgressMeter - pseudochrom_23:1222918 3.0 7310 2455.6
18:42:00.695 INFO ProgressMeter - pseudochrom_23:1305523 3.1 7790 2477.0
18:42:10.765 INFO ProgressMeter - pseudochrom_23:1457789 3.3 8680 2620.1
18:42:20.899 INFO ProgressMeter - pseudochrom_23:1636208 3.5 9750 2800.4
18:42:30.922 INFO ProgressMeter - pseudochrom_23:1780023 3.6 10640 2916.1
18:42:40.981 INFO ProgressMeter - pseudochrom_23:1955789 3.8 11720 3071.0
18:42:51.075 INFO ProgressMeter - pseudochrom_23:2108472 4.0 12660 3177.2
18:43:01.113 INFO ProgressMeter - pseudochrom_23:2286350 4.2 13710 3302.1
18:43:11.157 INFO ProgressMeter - pseudochrom_23:2484540 4.3 14930 3456.6
18:43:21.167 INFO ProgressMeter - pseudochrom_23:2607582 4.5 15660 3490.7
18:43:31.253 INFO ProgressMeter - pseudochrom_23:2779264 4.7 16750 3598.9
18:43:41.256 INFO ProgressMeter - pseudochrom_23:2958401 4.8 17840 3700.5
18:43:51.431 INFO ProgressMeter - pseudochrom_23:3091735 5.0 18670 3741.1
18:44:01.489 INFO ProgressMeter - pseudochrom_23:3256919 5.2 19650 3809.5
18:44:11.888 INFO ProgressMeter - pseudochrom_23:3395538 5.3 20500 3845.1
18:44:22.047 INFO ProgressMeter - pseudochrom_23:3496925 5.5 21130 3841.2
18:44:32.048 INFO ProgressMeter - pseudochrom_23:3647997 5.7 22050 3890.6
18:44:42.058 INFO ProgressMeter - pseudochrom_23:3770277 5.8 22830 3913.0
18:44:52.224 INFO ProgressMeter - pseudochrom_23:3855394 6.0 23350 3889.2
18:45:02.305 INFO ProgressMeter - pseudochrom_23:3961378 6.2 24000 3888.7
18:45:12.396 INFO ProgressMeter - pseudochrom_23:4077288 6.3 24700 3895.9
18:45:22.481 INFO ProgressMeter - pseudochrom_23:4209807 6.5 25510 3919.8
18:45:32.603 INFO ProgressMeter - pseudochrom_23:4301812 6.7 26100 3909.1
18:45:42.779 INFO ProgressMeter - pseudochrom_23:4400034 6.8 26720 3902.8
18:45:53.263 INFO ProgressMeter - pseudochrom_23:4475456 7.0 27180 3871.2
18:46:04.692 INFO ProgressMeter - pseudochrom_23:4607856 7.2 28000 3882.6
18:46:14.837 INFO ProgressMeter - pseudochrom_23:4739532 7.4 28790 3900.7
18:46:26.963 INFO ProgressMeter - pseudochrom_23:4805956 7.6 29230 3854.8
18:46:37.150 INFO ProgressMeter - pseudochrom_23:4932551 7.8 30010 3871.0
18:46:47.557 INFO ProgressMeter - pseudochrom_23:5051360 7.9 30750 3879.6
18:46:57.575 INFO ProgressMeter - pseudochrom_23:5156893 8.1 31410 3881.1
18:47:07.589 INFO ProgressMeter - pseudochrom_23:5256960 8.3 32020 3876.6
18:47:17.844 INFO ProgressMeter - pseudochrom_23:5339306 8.4 32520 3857.3
18:47:28.069 INFO ProgressMeter - pseudochrom_23:5447309 8.6 33170 3856.4
18:47:38.135 INFO ProgressMeter - pseudochrom_23:5562641 8.8 33870 3862.5
18:47:48.259 INFO ProgressMeter - pseudochrom_23:5648642 8.9 34390 3847.8
18:47:58.434 INFO ProgressMeter - pseudochrom_23:5750249 9.1 35010 3844.2
18:48:09.065 INFO ProgressMeter - pseudochrom_23:5853949 9.3 35650 3839.7
18:48:19.112 INFO ProgressMeter - pseudochrom_23:5955110 9.5 36280 3838.4
18:48:29.206 INFO ProgressMeter - pseudochrom_23:6051364 9.6 36860 3831.5
18:48:39.584 INFO ProgressMeter - pseudochrom_23:6140606 9.8 37400 3819.0
18:48:49.694 INFO ProgressMeter - pseudochrom_23:6228203 10.0 37930 3807.6
18:48:59.742 INFO ProgressMeter - pseudochrom_23:6327447 10.1 38550 3805.9
18:49:10.118 INFO ProgressMeter - pseudochrom_23:6412023 10.3 39070 3792.5
18:49:20.131 INFO ProgressMeter - pseudochrom_23:6528580 10.5 39780 3799.8
18:49:30.488 INFO ProgressMeter - pseudochrom_23:6664489 10.6 40640 3819.0
18:49:41.323 INFO ProgressMeter - pseudochrom_23:6776006 10.8 41330 3819.0
18:49:51.947 INFO ProgressMeter - pseudochrom_23:6871397 11.0 41910 3810.3
18:50:02.348 INFO ProgressMeter - pseudochrom_23:6965003 11.2 42470 3801.3
18:50:12.656 INFO ProgressMeter - pseudochrom_23:7064647 11.3 43070 3796.6
18:50:22.681 INFO ProgressMeter - pseudochrom_23:7129699 11.5 43450 3774.5
18:50:32.723 INFO ProgressMeter - pseudochrom_23:7217180 11.7 43990 3766.7
18:50:42.805 INFO ProgressMeter - pseudochrom_23:7334195 11.8 44720 3774.9
18:50:52.874 INFO ProgressMeter - pseudochrom_23:7470037 12.0 45560 3792.0
18:51:03.070 INFO ProgressMeter - pseudochrom_23:7580430 12.2 46240 3795.0
18:51:13.109 INFO ProgressMeter - pseudochrom_23:7703064 12.4 46990 3804.3
18:51:23.274 INFO ProgressMeter - pseudochrom_23:7839176 12.5 47810 3818.3
18:51:33.338 INFO ProgressMeter - pseudochrom_23:7960865 12.7 48540 3825.4
18:51:43.392 INFO ProgressMeter - pseudochrom_23:8028264 12.9 48960 3808.2
18:51:53.463 INFO ProgressMeter - pseudochrom_23:8151834 13.0 49710 3816.7
18:52:03.665 INFO ProgressMeter - pseudochrom_23:8270942 13.2 50430 3822.1
18:52:13.727 INFO ProgressMeter - pseudochrom_23:8359715 13.4 50970 3814.5
18:52:23.905 INFO ProgressMeter - pseudochrom_23:8477290 13.5 51650 3816.9
18:52:33.954 INFO ProgressMeter - pseudochrom_23:8594099 13.7 52380 3823.6
18:52:44.110 INFO ProgressMeter - pseudochrom_23:8710379 13.9 53100 3828.8
18:52:54.114 INFO ProgressMeter - pseudochrom_23:8848199 14.0 53970 3845.3
18:53:04.680 INFO ProgressMeter - pseudochrom_23:8983340 14.2 54800 3856.1
18:53:15.384 INFO ProgressMeter - pseudochrom_23:9068836 14.4 55310 3843.7
18:53:25.473 INFO ProgressMeter - pseudochrom_23:9222012 14.6 56240 3863.2
18:53:35.477 INFO ProgressMeter - pseudochrom_23:9305881 14.7 56750 3854.1
18:53:45.512 INFO ProgressMeter - pseudochrom_23:9431585 14.9 57500 3861.2
18:53:55.687 INFO ProgressMeter - pseudochrom_23:9550933 15.1 58210 3864.8
18:54:05.702 INFO ProgressMeter - pseudochrom_23:9694239 15.2 59090 3880.3
18:54:15.903 INFO ProgressMeter - pseudochrom_23:9779200 15.4 59620 3871.8
18:54:25.917 INFO ProgressMeter - pseudochrom_23:9884556 15.6 60260 3871.4
18:54:36.002 INFO ProgressMeter - pseudochrom_23:9991326 15.7 60900 3870.7
18:54:46.010 INFO ProgressMeter - pseudochrom_23:10127422 15.9 61710 3881.1
18:54:56.072 INFO ProgressMeter - pseudochrom_23:10247506 16.1 62430 3885.4
18:55:06.287 INFO ProgressMeter - pseudochrom_23:10372627 16.2 63210 3892.7
18:55:16.338 INFO ProgressMeter - pseudochrom_23:10508632 16.4 64040 3903.5
18:55:26.423 INFO ProgressMeter - pseudochrom_23:10605673 16.6 64630 3899.5
18:55:36.484 INFO ProgressMeter - pseudochrom_23:10680890 16.7 65090 3888.0
18:55:46.555 INFO ProgressMeter - pseudochrom_23:10755549 16.9 65530 3875.4
18:55:56.618 INFO ProgressMeter - pseudochrom_23:10860581 17.1 66160 3874.2
18:56:06.724 INFO ProgressMeter - pseudochrom_23:10958345 17.2 66750 3870.6
18:56:16.801 INFO ProgressMeter - pseudochrom_23:11078670 17.4 67480 3875.2
18:56:26.824 INFO ProgressMeter - pseudochrom_23:11172750 17.6 68070 3871.9
18:56:36.886 INFO ProgressMeter - pseudochrom_23:11297520 17.7 68800 3876.5
18:56:46.910 INFO ProgressMeter - pseudochrom_23:11394420 17.9 69390 3873.2
18:56:56.924 INFO ProgressMeter - pseudochrom_23:11466077 18.1 69840 3862.4
18:57:06.975 INFO ProgressMeter - pseudochrom_23:11575994 18.2 70500 3863.1
18:57:17.094 INFO ProgressMeter - pseudochrom_23:11713112 18.4 71340 3873.3
18:57:27.171 INFO ProgressMeter - pseudochrom_23:11835109 18.6 72080 3878.1
18:57:37.329 INFO ProgressMeter - pseudochrom_23:11907584 18.8 72540 3867.7
18:57:47.364 INFO ProgressMeter - pseudochrom_23:12031631 18.9 73340 3875.8
18:57:57.451 INFO ProgressMeter - pseudochrom_23:12122040 19.1 73890 3870.4
18:58:07.495 INFO ProgressMeter - pseudochrom_23:12238860 19.3 74590 3873.1
18:58:17.565 INFO ProgressMeter - pseudochrom_23:12364885 19.4 75350 3878.8
18:58:27.731 INFO ProgressMeter - pseudochrom_23:12451270 19.6 75890 3872.8
18:58:38.320 INFO ProgressMeter - pseudochrom_23:12537057 19.8 76410 3864.5
18:58:48.414 INFO ProgressMeter - pseudochrom_23:12580452 19.9 76650 3844.0
18:58:59.346 INFO ProgressMeter - pseudochrom_23:12630247 20.1 76930 3823.1
18:59:10.085 INFO ProgressMeter - pseudochrom_23:12746384 20.3 77510 3818.0
18:59:20.474 INFO ProgressMeter - pseudochrom_23:12814970 20.5 77930 3806.2
18:59:30.683 INFO ProgressMeter - pseudochrom_23:12833522 20.6 78040 3780.1
18:59:41.531 INFO ProgressMeter - pseudochrom_23:12867911 20.8 78220 3756.0
18:59:51.979 INFO ProgressMeter - pseudochrom_23:12898083 21.0 78380 3732.4
19:00:02.811 INFO ProgressMeter - pseudochrom_23:12912010 21.2 78460 3704.4
19:00:12.854 INFO ProgressMeter - pseudochrom_23:12954239 21.3 78720 3687.5
19:00:23.618 INFO ProgressMeter - pseudochrom_23:13045215 21.5 79170 3677.7
19:00:33.765 INFO ProgressMeter - pseudochrom_23:13113654 21.7 79520 3665.2
19:00:46.176 INFO ProgressMeter - pseudochrom_23:13230637 21.9 80100 3657.0
19:00:57.561 INFO ProgressMeter - pseudochrom_23:13254119 22.1 80230 3631.5
19:01:11.951 INFO ProgressMeter - pseudochrom_23:13277140 22.3 80370 3598.8
19:01:23.954 INFO ProgressMeter - pseudochrom_23:13291793 22.5 80450 3570.4
19:01:34.143 INFO ProgressMeter - pseudochrom_23:13313750 22.7 80580 3549.4
19:01:44.470 INFO ProgressMeter - pseudochrom_23:13410560 22.9 81090 3545.0
19:01:54.793 INFO ProgressMeter - pseudochrom_23:13469784 23.0 81440 3533.7
19:02:05.477 INFO ProgressMeter - pseudochrom_23:13499022 23.2 81590 3513.1
19:02:15.584 INFO ProgressMeter - pseudochrom_23:13574066 23.4 81950 3503.2
19:02:27.238 INFO ProgressMeter - pseudochrom_23:13603519 23.6 82110 3481.1
19:02:37.410 INFO ProgressMeter - pseudochrom_23:13625698 23.8 82240 3461.7
19:02:48.228 INFO ProgressMeter - pseudochrom_23:13691826 23.9 82570 3449.4
19:02:59.032 INFO ProgressMeter - pseudochrom_23:13757035 24.1 82950 3439.4
19:03:09.114 INFO ProgressMeter - pseudochrom_23:13779661 24.3 83100 3421.8
19:03:19.416 INFO ProgressMeter - pseudochrom_23:13820635 24.5 83330 3407.2
19:03:29.183 INFO HaplotypeCaller - 55869059 read(s) filtered by: ((((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND GoodCigarReadFilter) AND WellformedReadFilter)
55869059 read(s) filtered by: (((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND GoodCigarReadFilter)
55869059 read(s) filtered by: ((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter)
55869059 read(s) filtered by: (((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter)
55869059 read(s) filtered by: ((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter)
47376329 read(s) filtered by: (((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter)
46853127 read(s) filtered by: ((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter)
46853127 read(s) filtered by: (MappingQualityReadFilter AND MappingQualityAvailableReadFilter)
46853127 read(s) filtered by: MappingQualityReadFilter
523202 read(s) filtered by: NotSecondaryAlignmentReadFilter
8492730 read(s) filtered by: NotDuplicateReadFilter
19:03:29.184 INFO ProgressMeter - pseudochrom_23:13859898 24.6 83586 3395.1
19:03:29.184 INFO ProgressMeter - Traversal complete. Processed 83586 total regions in 24.6 minutes.
19:03:30.381 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
19:03:30.381 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.0
19:03:30.381 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.00 sec
19:03:30.381 INFO HaplotypeCaller - Shutting down engine
[July 4, 2018 7:03:30 PM CST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 24.73 minutes.
Runtime.totalMemory()=372873625
and the result *.gvcf:
##fileformat=VCFv4.2
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##FILTER=<ID=LowQual,Description="Low quality">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --dbsnp /path/to/dbsnp/sample.dbsnp.vcf --emit-ref-confidence GVCF --output /path/to/result/sample.g.vcf --input /path/to/BQSR/sample.bqsr.bam --reference /path/to/index/chrom23.fasta --TMP_DIR /path/to/tmp --annotation-group StandardAnnotation --annotation-group StandardHCAnnotation --disable-tool-default-annotations false --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --recover-dangling-heads false --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false --minimum-mapping-quality 20",Version=4.0.4.0,Date="July 4, 2018 6:38:51 PM CST">
##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive)
##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive)
##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive)
##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive)
##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive)
##GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive)
##GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive)
##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive)
##GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive)
##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive)
##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive)
##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive)
##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive)
##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive)
##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive)
##GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive)
##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive)
##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive)
##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive)
##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive)
##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive)
##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive)
##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive)
##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive)
##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive)
##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive)
##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive)
##GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive)
##GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive)
##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive)
##GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive)
##GVCFBlock37-38=minGQ=37(inclusive),maxGQ=38(exclusive)
##GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive)
##GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive)
##GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive)
##GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive)
##GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive)
##GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive)
##GVCFBlock43-44=minGQ=43(inclusive),maxGQ=44(exclusive)
##GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive)
##GVCFBlock45-46=minGQ=45(inclusive),maxGQ=46(exclusive)
##GVCFBlock46-47=minGQ=46(inclusive),maxGQ=47(exclusive)
##GVCFBlock47-48=minGQ=47(inclusive),maxGQ=48(exclusive)
##GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive)
##GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive)
##GVCFBlock5-6=minGQ=5(inclusive),maxGQ=6(exclusive)
##GVCFBlock50-51=minGQ=50(inclusive),maxGQ=51(exclusive)
##GVCFBlock51-52=minGQ=51(inclusive),maxGQ=52(exclusive)
##GVCFBlock52-53=minGQ=52(inclusive),maxGQ=53(exclusive)
##GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive)
##GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive)
##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive)
##GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive)
##GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive)
##GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive)
##GVCFBlock59-60=minGQ=59(inclusive),maxGQ=60(exclusive)
##GVCFBlock6-7=minGQ=6(inclusive),maxGQ=7(exclusive)
##GVCFBlock60-70=minGQ=60(inclusive),maxGQ=70(exclusive)
##GVCFBlock7-8=minGQ=7(inclusive),maxGQ=8(exclusive)
##GVCFBlock70-80=minGQ=70(inclusive),maxGQ=80(exclusive)
##GVCFBlock8-9=minGQ=8(inclusive),maxGQ=9(exclusive)
##GVCFBlock80-90=minGQ=80(inclusive),maxGQ=90(exclusive)
##GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive)
##GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive)
##GVCFBlock99-100=minGQ=99(inclusive),maxGQ=100(exclusive)
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##contig=<ID=pseudochrom_23,length=13860564>
##source=HaplotypeCaller
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CL100020307_L01_17
pseudochrom_23 1 . A <NON_REF> . . END=13860564 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
I don't know if it's reasonable to suppose that there must be some variation, as the dbsnp vcf file contained 11733 variation. Even if there is no variation, HaplotypeCaller should output all recode like position 1. But there is nothing.