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HaplotypeCaller output header and one position recode without error

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 [email protected] 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.">
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##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive)
##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive)
##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive)
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##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive)
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##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive)
##GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive)
##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive)
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##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.

Comments

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @hankai,

    In general, the --dbsnp file is only used to populate the ID column of the output and does not contribute to analysis otherwise. Can you check that your dbsnp file contain variants for pseudochrom_23?

    It looks like your entire pseudochrom_23 contig is a block without any variation. If you look at your alignments in IGV, do you see variation?

  • hankaihankai Member

    The dbsnp file I used (only) contained variation for pseudochrom_23.

    I viewed the *.bqsr.bam alignment using IGV and found some variation exists.

    I don't think it's a cause of NONE-variation, as some paralleled sample have correct output with all <NON_REF> record line in vcf body.

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @hankai,

    Your alignments don't look right. The reads with the rainbow striping indicate massive mismatches that typically indicate reference-to-sample mismatch. In the middle of your IGV screenshot, you have a pileup without the rainbow striping but the coverage chart shows many mismatches as well as uneven coverage. Here are some things to check for.

    1. Check you've loaded the correct reference to IGV. We all occasionally load data to the wrong reference.
    2. Check you've aligned to the correct reference. Happens.
    3. Sample swaps are more common than you think. BLAST some of your reads to see if the data are what you expect.
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