Hi GATK support,

I am trying to use gatk4 combineGVCFs to combine two individual gvcf files for joint calling and found that CombineGVCFs gives wrong allelic depth. Here is the example:

For locus 2:182816563 it is homozygous reference with reference allelic depth=57 and alternative non reference allelic depth=2
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  Sample1
2       182816563       .       T       <NON_REF>       .       .       .       GT:AD:DP:GQ:PL  0/0:57,2:59:99:0,120,1800

For the same locus in another sample, there is an indel present. 

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  Sample2

2       182816563       .       TCTTTA  T,<NON_REF>     2533.73 .       AS_RAW_BaseQRankSum=|-1.1,1|NaN;AS_RAW_MQ=190800.00|234000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|3.1,1|NaN;AS_SB_TABLE=36,17|41,24|0,0;BaseQRankSum=-1.030;DP=121;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=435600.00;ReadPosRankSum=3.176       GT:AD:GQ:PL:SB  0/1:53,65,0:99:2571,0,3497,2730,3693,6423:36,17,41,24

When I used combineGVCF to combine this locus from two samples, I found that the allelic depth for Sample 1 was wrongly assigned as 57,2,2. The reasons why I think it is wrong:
1. This allelic depth does not add to the overall allelic depth 59.

2. There is no deletion at this locus for sample 2. But the allelic depth shows that for Alternative allele T, the allelic depth is 2. 

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  Sample2 Sample1

2       182816563       .       TCTTTA  T,<NON_REF>     .       .       AS_RAW_BaseQRankSum=|-1.1,1|;AS_RAW_MQ=190800.00|234000.00|0.00;AS_RAW_MQRankSum=|0.0,1|;AS_RAW_ReadPosRankSum=|3.1,1|;AS_SB_TABLE=36,17|41,24|0,0;BaseQRankSum=-1.030e+00;DP=180;ExcessHet=3.01;MQRankSum=0.00;RAW_MQ=435600.00;ReadPosRankSum=3.18   GT:AD:DP:GQ:PL:SB       ./.:53,65,0:.:99:2571,0,3497,2730,3693,6423:36,17,41,24./.:57,2,2:59:99:0,120,1800,120,1800,1800

I would really appreciate your help in this issue. Thank you!

GATK version used: gatk4-4.3.0.0-0
Exact command used: gatk CombineGVCFs  -R $miller/ref/hs37d5/hs37d5.fa -V 1278_heart_bulk.g.vcf.gz -V 1278BA9-A.g.vcf.gz -O combine2.vcf.gz -G StandardAnnotation -G AS_StandardAnnotation
Entire program log:
Using GATK jar /home/boj924/miniconda3/envs/scan2/share/gatk4-4.3.0.0-0/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 -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -jar /home/boj924/miniconda3/envs/scan2/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar CombineGVCFs -R /n/data1/bwh/pathology/miller/lab/ref/hs37d5/hs37d5.fa -V 1278_heart_bulk.g.vcf.gz -V 1278BA9-A.g.vcf.gz -O combine2.vcf.gz -G StandardAnnotation -G AS_StandardAnnotation
14:19:48.385 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation group (StandardAnnotation) is enabled for this tool by default
14:19:48.496 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/boj924/miniconda3/envs/scan2/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
14:19:48.807 INFO  CombineGVCFs - ------------------------------------------------------------
14:19:48.807 INFO  CombineGVCFs - The Genome Analysis Toolkit (GATK) v4.3.0.0
14:19:48.807 INFO  CombineGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
14:19:48.808 INFO  CombineGVCFs - Executing as boj924@compute-a-16-171.o2.rc.hms.harvard.edu on Linux v3.10.0-1160.102.1.el7.x86_64 amd64
14:19:48.808 INFO  CombineGVCFs - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_332-b09
14:19:48.808 INFO  CombineGVCFs - Start Date/Time: January 11, 2024 2:19:48 PM EST
14:19:48.808 INFO  CombineGVCFs - ------------------------------------------------------------
14:19:48.808 INFO  CombineGVCFs - ------------------------------------------------------------
14:19:48.809 INFO  CombineGVCFs - HTSJDK Version: 3.0.1
14:19:48.809 INFO  CombineGVCFs - Picard Version: 2.27.5
14:19:48.809 INFO  CombineGVCFs - Built for Spark Version: 2.4.5
14:19:48.809 INFO  CombineGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:19:48.809 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:19:48.809 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:19:48.810 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:19:48.810 INFO  CombineGVCFs - Deflater: IntelDeflater
14:19:48.810 INFO  CombineGVCFs - Inflater: IntelInflater
14:19:48.810 INFO  CombineGVCFs - GCS max retries/reopens: 20
14:19:48.810 INFO  CombineGVCFs - Requester pays: disabled
14:19:48.810 INFO  CombineGVCFs - Initializing engine
14:19:49.600 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/boj924/AD_Tau_PTA/1278_heart_bulk.g.vcf.gz
14:19:49.630 WARN  IntelInflater - Zero Bytes Written : 0
14:19:49.652 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/boj924/AD_Tau_PTA/1278BA9-A.g.vcf.gz
14:19:49.663 WARN  IntelInflater - Zero Bytes Written : 0
14:19:49.686 WARN  IntelInflater - Zero Bytes Written : 0
14:19:49.704 WARN  IntelInflater - Zero Bytes Written : 0
14:19:49.900 INFO  CombineGVCFs - Done initializing engine
14:19:49.939 INFO  ProgressMeter - Starting traversal
14:19:49.939 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:19:49.942 WARN  IntelInflater - Zero Bytes Written : 0
14:19:49.973 WARN  IntelInflater - Zero Bytes Written : 0
14:19:50.068 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 2:182816563 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
14:19:50.099 INFO  ProgressMeter -             unmapped              0.0                    22           8250.0
14:19:50.099 INFO  ProgressMeter - Traversal complete. Processed 22 total variants in 0.0 minutes.
14:19:50.118 INFO  CombineGVCFs - Shutting down engine
[January 11, 2024 2:19:50 PM EST] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=324534272