Hello.

Thank you for your support.

FYI, this is not a meaningless iteration of https://gatk.broadinstitute.org/hc/en-us/community/posts/4407873427355-Deletion-is-split-into-two-deletions, because the problem doesn't seems to have been properly addressed at the time.

 A long deletion, specifically EGFR exon 19 deletion (a 18-base del), is split into a 10-base del + a 2 matching nucletides + 8-base del. The problem seems to arise from trying to resolve the nearby SNV.

1. Link for IGV snapshot of the problematic site (with the 18-base del right next to a perfectly-phased C>A substitution 2 bases away.)

    Top view: input alignment

    Bottom view: Bam output produced by Mutect2 --bam-output flag

2. The VCF call

chr7    55242468    .    ATTAAGAGAAG    A    .    .    AS_SB_TABLE=1180,978|233,190;DP=2829;ECNT=4;ECNTH=4;MBQ=20,34;MFRL=105,141;MMQ=60,60;MPOS=35;POPAF=7.30
;TLOD=1455.14    GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB    0|1:2158,423:0.192:2581:472,120:572,139:1452,341:0|1:55242468_ATTAAGAGAAG_A:55242468:1180,978,233,190
chr7    55242480    .    AACATCTCC    A    .    .    AS_SB_TABLE=1212,991|232,190;DP=2721;ECNT=4;ECNTH=4;MBQ=20,36;MFRL=104,141;MMQ=60,60;MPOS=35;POPAF=7.30
;TLOD=1451.57    GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB    0|1:2203,422:0.188:2625:508,105:592,131:1478,340:0|1:55242468_ATTAAGAGAAG_A:55242468:1212,991,232,190

REQUIRED for all errors and issues:
a) GATK version used: 4.6.0.0
b) Exact command used: 

gatk --java-options "-Xmx32G" Mutect2 \
-R $REF \
-L target_baits.bed \
-I $BAM \
--germline-resource /home/disk/PublicData/gnomAD/af-only-gnomad_genomes_v4.1_hg19.vcf.gz \
--panel-of-normals /home/disk/PublicData/PanelOfNormals/somatic-b37tohg19_Mutect2-WGS-panel-hg19.vcf \
-O $OUT_DIR/$SMPL.vcf.gz \
--max-assembly-region-size 500 \
--linked-de-bruijn-graph \
--debug-assembly true \
--recover-all-dangling-branches \
--max-mnp-distance 5 \
--tumor-lod-to-emit 2.0 \
--dont-use-soft-clipped-bases true \
--minimum-allele-fraction 0.0 \
--genotype-germline-sites true \
--genotype-pon-sites true \
--interval-padding 100

c) Entire program log:

      3 Using GATK jar /opt/GATK/gatk-4.6.0.0/gatk-package-4.6.0.0-local.jar
      4 Running:
      5     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 -Xm
      6 20:50:55.083 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/GATK/gatk-4.6.0.0/gatk-package-4.6.0.0-local.jar!/com/intel/gkl/native/libgkl
      7 20:50:55.255 INFO  Mutect2 - ------------------------------------------------------------
      8 20:50:55.260 INFO  Mutect2 - The Genome Analysis Toolkit (GATK) v4.6.0.0
      9 20:50:55.260 INFO  Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
     10 20:50:55.261 INFO  Mutect2 - Executing as soh1@tgils2 on Linux v3.10.0-957.el7.x86_64 amd64
     11 20:50:55.261 INFO  Mutect2 - Java runtime: Java HotSpot(TM) 64-Bit Server VM v17.0.10+11-LTS-240
     12 20:50:55.261 INFO  Mutect2 - Start Date/Time: November 19, 2024 at 8:50:55 PM KST
     13 20:50:55.261 INFO  Mutect2 - ------------------------------------------------------------
     14 20:50:55.261 INFO  Mutect2 - ------------------------------------------------------------
     15 20:50:55.263 INFO  Mutect2 - HTSJDK Version: 4.1.1
     16 20:50:55.263 INFO  Mutect2 - Picard Version: 3.2.0
     17 20:50:55.263 INFO  Mutect2 - Built for Spark Version: 3.5.0
     18 20:50:55.264 INFO  Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
     19 20:50:55.264 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
     20 20:50:55.264 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
     21 20:50:55.264 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
     22 20:50:55.265 INFO  Mutect2 - Deflater: IntelDeflater
     23 20:50:55.265 INFO  Mutect2 - Inflater: IntelInflater
     24 20:50:55.265 INFO  Mutect2 - GCS max retries/reopens: 20
     25 20:50:55.265 INFO  Mutect2 - Requester pays: disabled
     26 20:50:55.266 INFO  Mutect2 - Initializing engine
     27 20:50:55.468 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/disk/PublicData/PanelOfNormals/somatic-b37tohg19_Mutect2-WGS-panel-hg19.vcf
     28 20:50:55.679 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/disk/PublicData/gnomAD/af-only-gnomad_genomes_v4.1_hg19.vcf.gz
     29 20:50:55.821 INFO  FeatureManager - Using codec BEDCodec to read file file:///home/disk/projects/NSCLC-MinorClone/TST500_manifest/TST500C_EGFRex19del.bed
     30 20:50:55.827 INFO  IntervalArgumentCollection - Processing 303 bp from intervals
     31 20:50:55.835 INFO  Mutect2 - Done initializing engine
     32 20:50:55.843 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/opt/GATK/gatk-4.6.0.0/gatk-package-4.6.0.0-local.jar!/com/intel/gkl/native/libgkl_utils
     33 20:50:55.844 INFO  NativeLibraryLoader - Loading libgkl_smithwaterman.so from jar:file:/opt/GATK/gatk-4.6.0.0/gatk-package-4.6.0.0-local.jar!/com/intel/gkl/native/libg
     34 20:50:55.845 INFO  IntelSmithWaterman - Using CPU-supported AVX-512 instructions
     35 20:50:55.845 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
     36 20:50:55.852 ERROR ReadThreadingAssembler - JunctionTreeLinkedDeBruijnGraph is enabled.
     37  This is an experimental assembly graph mode that has not been fully validated
     38 
     39 
     40 20:50:55.858 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/opt/GATK/gatk-4.6.0.0/gatk-package-4.6.0.0-local.jar!/com/intel/gkl/native/libgkl
     41 20:50:55.889 INFO  IntelPairHmm - Using CPU-supported AVX-512 instructions
     42 20:50:55.889 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
     43 20:50:55.889 INFO  IntelPairHmm - Available threads: 36
     44 20:50:55.889 INFO  IntelPairHmm - Requested threads: 4
     45 20:50:55.889 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
     46 20:50:55.926 INFO  ProgressMeter - Starting traversal
     47 20:50:55.926 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Regions Processed   Regions/Minute
     48 20:50:57.187 INFO  Mutect2Engine - Assembling chr7:55242383-55242615 with 12396 reads:    (with overlap region = chr7:55242283-55242715)
     49 20:50:57.502 INFO  ReadThreadingAssembler - Using kmer size of 10 in read threading assembler
     50 20:50:57.631 INFO  ReadThreadingAssembler - Using kmer size of 25 in read threading assembler
     51 20:50:57.810 INFO  ReadThreadingAssembler - Adding haplotype 433M from graph with kmer 25
     52 20:50:57.812 INFO  ReadThreadingAssembler - Adding haplotype 186M10D2M8D227M from graph with kmer 25
     53 20:50:57.812 INFO  ReadThreadingAssembler - Adding haplotype 186M10D2M8D227M from graph with kmer 25
     54 20:50:57.813 INFO  ReadThreadingAssembler - Adding haplotype 433M from graph with kmer 25
     55 20:50:57.813 INFO  ReadThreadingAssembler - Adding haplotype 186M10D2M8D227M from graph with kmer 25
     56 20:50:57.814 INFO  ReadThreadingAssembler - Adding haplotype 186M10D2M8D227M from graph with kmer 25
     57 20:50:57.815 INFO  ReadThreadingAssembler - Found 6 candidate haplotypes of 6 possible combinations to evaluate every read against.
     58 20:50:57.815 INFO  ReadThreadingAssembler - GGTGCGGCTCCACAGCCCCAGTGTCCCTCACCTTCGGGGTGCATCGCTGGTAACATCCACCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCT
     59 20:50:57.819 INFO  ReadThreadingAssembler - > Cigar = 433M : 433 score -0.12124612672119461 ref false
     60 20:50:57.819 INFO  ReadThreadingAssembler - GGTGCGGCTCCACAGCCCCAGTGTCCCTCACCTTCGGGGTGCATCGCTGGTAACATCCACCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCT
     61 20:50:57.819 INFO  ReadThreadingAssembler - > Cigar = 186M10D2M8D227M : 433 score -0.6315012207074924 ref false
     62 20:50:57.819 INFO  ReadThreadingAssembler - GGTGCGGCTCCACAGCCCCAGTGTCCCTCACCTTCGGGGTGCATCGCTGGTAACATCCACCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCT
     63 20:50:57.819 INFO  ReadThreadingAssembler - > Cigar = 186M10D2M8D227M : 433 score -2.041517679566783 ref false
     64 20:50:57.819 INFO  ReadThreadingAssembler - GGTGCGGCTCCACAGCCCCAGTGTCCCTCACCTTCGGGGTGCATCGCTGGTAACATCCACCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCT
     65 20:50:57.819 INFO  ReadThreadingAssembler - > Cigar = 186M10D2M8D227M : 433 score -3.6799430242578968 ref false
     66 20:50:57.819 INFO  ReadThreadingAssembler - GGTGCGGCTCCACAGCCCCAGTGTCCCTCACCTTCGGGGTGCATCGCTGGTAACATCCACCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCT
     67 20:50:57.819 INFO  ReadThreadingAssembler - > Cigar = 186M10D2M8D227M : 433 score -5.0899594831171875 ref false
     68 20:50:57.819 INFO  ReadThreadingAssembler - GGTGCGGCTCCACAGCCCCAGTGTCCCTCACCTTCGGGGTGCATCGCTGGTAACATCCACCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCT
     69 20:50:57.820 INFO  ReadThreadingAssembler - > Cigar = 433M : 433 score NaN ref true
     70 20:50:57.822 INFO  EventMap - === Best Haplotypes ===
     71 20:50:57.823 INFO  EventMap - GGTGCGGCTCCACAGCCCCAGTGTCCCTCACCTTCGGGGTGCATCGCTGGTAACATCCACCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACT
     72 20:50:57.823 INFO  EventMap - > Cigar = 433M
     73 20:50:57.823 INFO  EventMap - >> Events = EventMap{}
     74 20:50:57.823 INFO  EventMap - GGTGCGGCTCCACAGCCCCAGTGTCCCTCACCTTCGGGGTGCATCGCTGGTAACATCCACCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACT
     75 20:50:57.823 INFO  EventMap - > Cigar = 433M
     76 20:50:57.823 INFO  EventMap - >> Events = EventMap{chr7:55242609-55242609 [A*, G],}
     77 20:50:57.823 INFO  EventMap - GGTGCGGCTCCACAGCCCCAGTGTCCCTCACCTTCGGGGTGCATCGCTGGTAACATCCACCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACT
     78 20:50:57.823 INFO  EventMap - > Cigar = 186M10D2M8D227M
     79 20:50:57.824 INFO  EventMap - >> Events = EventMap{chr7:55242468-55242478 [ATTAAGAGAAG*, A],chr7:55242480-55242488 [AACATCTCC*, A],chr7:55242609-55242609 [A*, G],}
     80 20:50:57.824 INFO  EventMap - GGTGCGGCTCCACAGCCCCAGTGTCCCTCACCTTCGGGGTGCATCGCTGGTAACATCCACCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACT
     81 20:50:57.824 INFO  EventMap - > Cigar = 186M10D2M8D227M
     82 20:50:57.824 INFO  EventMap - >> Events = EventMap{chr7:55242456-55242456 [C*, A],chr7:55242468-55242478 [ATTAAGAGAAG*, A],chr7:55242480-55242488 [AACATCTCC*, A],chr7:
     83 20:50:57.824 INFO  EventMap - GGTGCGGCTCCACAGCCCCAGTGTCCCTCACCTTCGGGGTGCATCGCTGGTAACATCCACCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACT
     84 20:50:57.824 INFO  EventMap - > Cigar = 186M10D2M8D227M
     85 20:50:57.824 INFO  EventMap - >> Events = EventMap{chr7:55242468-55242478 [ATTAAGAGAAG*, A],chr7:55242480-55242488 [AACATCTCC*, A],}
     86 20:50:57.824 INFO  EventMap - GGTGCGGCTCCACAGCCCCAGTGTCCCTCACCTTCGGGGTGCATCGCTGGTAACATCCACCCAGATCACTGGGCAGCATGTGGCACCATCTCACAATTGCCAGTTAACGTCTTCCTTCTCTCTCTGTCATAGGGACT
     87 20:50:57.824 INFO  EventMap - > Cigar = 186M10D2M8D227M
     88 20:50:57.824 INFO  EventMap - >> Events = EventMap{chr7:55242456-55242456 [C*, A],chr7:55242468-55242478 [ATTAAGAGAAG*, A],chr7:55242480-55242488 [AACATCTCC*, A],}
     89 20:50:57.851 INFO  AssemblyResultSet - Trimming active region AssemblyRegion chr7:55242383-55242615 active?=true nReads=12396 with 6 haplotypes
     90 20:50:57.852 INFO  AssemblyResultSet - Trimmed region to chr7:55242393-55242629 and reduced number of haplotypes from 6 to only 6
     91 20:50:57.853 INFO  AssemblyResultSet - Remains: CTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATTCCCGTAGCTATCAAGGAACAGAAAGCCAACAAGGAAATCCTCGATGTGAGTTTCTGCTTTG
     92 20:50:57.853 INFO  AssemblyResultSet - Remains: CTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATTCCCGTAGCTATCAAGGAACAGAAAGCCAACAAGGAAATCCTCGATGTGAGTTTCTGCTTTG
     93 20:50:57.853 INFO  AssemblyResultSet - Remains: CTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATTCCCGTCGCTATCAAGGAACAGAAAGCCAACAAGGAAATCCTCGATGTGAGTTTCTGCTTTG
     94 20:50:57.853 INFO  AssemblyResultSet - Remains: CTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATTCCCGTCGCTATCAAGGAACAGAAAGCCAACAAGGAAATCCTCGATGTGAGTTTCTGCTTTG
     95 20:50:57.853 INFO  AssemblyResultSet - Remains: CTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATTCCCGTCGCTATCAAGGAATTAAGAGAAGCAACATCTCCGAAAGCCAACAAGGAAATCCTCG
     96 20:50:57.853 INFO  AssemblyResultSet - Remains: CTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATTCCCGTCGCTATCAAGGAATTAAGAGAAGCAACATCTCCGAAAGCCAACAAGGAAATCCTCG
     97 20:50:58.358 INFO  EventMap - === Best Haplotypes ===
     98 20:50:58.358 INFO  EventMap - CTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATTCCCGTAGCTATCAAGGAACAGAAAGCCAACAAGGAAATCCTCGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGG
     99 20:50:58.358 INFO  EventMap - > Cigar = 76M10D2M8D141M
    100 20:50:58.359 INFO  EventMap - >> Events = EventMap{chr7:55242456-55242456 [C*, A],chr7:55242468-55242478 [ATTAAGAGAAG*, A],chr7:55242480-55242488 [AACATCTCC*, A],}
    101 20:50:58.359 INFO  EventMap - CTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATTCCCGTAGCTATCAAGGAACAGAAAGCCAACAAGGAAATCCTCGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGG
    102 20:50:58.359 INFO  EventMap - > Cigar = 76M10D2M8D141M
    103 20:50:58.359 INFO  EventMap - >> Events = EventMap{chr7:55242456-55242456 [C*, A],chr7:55242468-55242478 [ATTAAGAGAAG*, A],chr7:55242480-55242488 [AACATCTCC*, A],chr7:
    104 20:50:58.359 INFO  EventMap - CTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATTCCCGTCGCTATCAAGGAACAGAAAGCCAACAAGGAAATCCTCGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGG
    105 20:50:58.359 INFO  EventMap - > Cigar = 76M10D2M8D141M
    106 20:50:58.359 INFO  EventMap - >> Events = EventMap{chr7:55242468-55242478 [ATTAAGAGAAG*, A],chr7:55242480-55242488 [AACATCTCC*, A],}
    107 20:50:58.359 INFO  EventMap - CTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATTCCCGTCGCTATCAAGGAACAGAAAGCCAACAAGGAAATCCTCGATGTGAGTTTCTGCTTTGCTGTGTGGGGGTCCATGG
    108 20:50:58.359 INFO  EventMap - > Cigar = 76M10D2M8D141M
    109 20:50:58.359 INFO  EventMap - >> Events = EventMap{chr7:55242468-55242478 [ATTAAGAGAAG*, A],chr7:55242480-55242488 [AACATCTCC*, A],chr7:55242609-55242609 [A*, G],}
    110 20:50:58.359 INFO  EventMap - CTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATTCCCGTCGCTATCAAGGAATTAAGAGAAGCAACATCTCCGAAAGCCAACAAGGAAATCCTCGATGTGAGTTTCTGCTTTG
    111 20:50:58.359 INFO  EventMap - > Cigar = 237M
    112 20:50:58.359 INFO  EventMap - >> Events = EventMap{}
    113 20:50:58.359 INFO  EventMap - CTTCCTTCTCTCTCTGTCATAGGGACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATTCCCGTCGCTATCAAGGAATTAAGAGAAGCAACATCTCCGAAAGCCAACAAGGAAATCCTCGATGTGAGTTTCTGCTTTG
    114 20:50:58.359 INFO  EventMap - > Cigar = 237M
    115 20:50:58.359 INFO  EventMap - >> Events = EventMap{chr7:55242609-55242609 [A*, G],}
    116 20:50:58.690 INFO  Mutect2 - 345 read(s) filtered by: MappingQualityReadFilter 
    117 0 read(s) filtered by: MappingQualityAvailableReadFilter 
    118 0 read(s) filtered by: MappingQualityNotZeroReadFilter 
    119 0 read(s) filtered by: MappedReadFilter 
    120 0 read(s) filtered by: NotSecondaryAlignmentReadFilter 
    121 0 read(s) filtered by: NotDuplicateReadFilter 
    122 0 read(s) filtered by: PassesVendorQualityCheckReadFilter 
    123 0 read(s) filtered by: NonChimericOriginalAlignmentReadFilter 
    124 0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter 
    125 0 read(s) filtered by: ReadLengthReadFilter 
    126 0 read(s) filtered by: GoodCigarReadFilter 
    127 0 read(s) filtered by: WellformedReadFilter 
    128 345 total reads filtered out of 14583 reads processed
    129 20:50:58.691 INFO  ProgressMeter -             unmapped              0.0                     2             43.4
    130 20:50:58.691 INFO  ProgressMeter - Traversal complete. Processed 2 total regions in 0.0 minutes.
    131 20:50:58.697 INFO  VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009516344000000001
    132 20:50:58.697 INFO  PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.212008306
    133 20:50:58.697 INFO  SmithWatermanAligner - Total compute time in native Smith-Waterman : 0.02 sec
    134 20:50:58.698 INFO  Mutect2 - Shutting down engine
    135 [November 19, 2024 at 8:50:58 PM KST] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.06 minutes.
    136 Runtime.totalMemory()=1157627904
    137 Tool returned:
    138 SUCCESS
    139 Completed Mutect2 run
    140 Running FilterMutectCalls for SS2238275D
    141 Using GATK jar /opt/GATK/gatk-4.6.0.0/gatk-package-4.6.0.0-local.jar
    142 Running:
    143     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 -ja
    144 20:51:00.935 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/GATK/gatk-4.6.0.0/gatk-package-4.6.0.0-local.jar!/com/intel/gkl/native/libgkl
    145 20:51:01.059 INFO  FilterMutectCalls - ------------------------------------------------------------
    146 20:51:01.067 INFO  FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.6.0.0
    147 20:51:01.067 INFO  FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
    148 20:51:01.068 INFO  FilterMutectCalls - Executing as soh1@tgils2 on Linux v3.10.0-957.el7.x86_64 amd64
    149 20:51:01.068 INFO  FilterMutectCalls - Java runtime: Java HotSpot(TM) 64-Bit Server VM v17.0.10+11-LTS-240
    150 20:51:01.070 INFO  FilterMutectCalls - Start Date/Time: November 19, 2024 at 8:51:00 PM KST
    151 20:51:01.070 INFO  FilterMutectCalls - ------------------------------------------------------------
    152 20:51:01.070 INFO  FilterMutectCalls - ------------------------------------------------------------
    153 20:51:01.073 INFO  FilterMutectCalls - HTSJDK Version: 4.1.1
    154 20:51:01.074 INFO  FilterMutectCalls - Picard Version: 3.2.0
    155 20:51:01.074 INFO  FilterMutectCalls - Built for Spark Version: 3.5.0
    156 20:51:01.074 INFO  FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    157 20:51:01.075 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    158 20:51:01.075 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    159 20:51:01.075 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    160 20:51:01.075 INFO  FilterMutectCalls - Deflater: IntelDeflater
    161 20:51:01.076 INFO  FilterMutectCalls - Inflater: IntelInflater
    162 20:51:01.076 INFO  FilterMutectCalls - GCS max retries/reopens: 20
    163 20:51:01.076 INFO  FilterMutectCalls - Requester pays: disabled
    164 20:51:01.077 INFO  FilterMutectCalls - Initializing engine
    165 20:51:01.204 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/disk/projects/NSCLC-MinorClone/bulk_sequencing/PyClone_Analysis/TEST_VCFs/SS2238275D
    166 20:51:01.235 INFO  FeatureManager - Using codec BEDCodec to read file file:///home/disk/projects/NSCLC-MinorClone/TST500_manifest/TST500C_EGFRex19del.bed
    167 20:51:01.244 INFO  IntervalArgumentCollection - Processing 303 bp from intervals
    168 20:51:01.254 INFO  FilterMutectCalls - Done initializing engine
    169 20:51:01.350 INFO  ProgressMeter - Starting traversal
    170 20:51:01.351 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
    171 20:51:01.352 INFO  FilterMutectCalls - Starting pass 0 through the variants
    172 20:51:01.439 INFO  FilterMutectCalls - Finished pass 0 through the variants
    173 20:51:01.454 INFO  FilterMutectCalls - Starting pass 1 through the variants
    174 20:51:01.463 INFO  FilterMutectCalls - Finished pass 1 through the variants
    175 20:51:01.464 INFO  FilterMutectCalls - Starting pass 2 through the variants
    176 20:51:01.472 INFO  FilterMutectCalls - Finished pass 2 through the variants
    177 20:51:01.472 INFO  FilterMutectCalls - Starting pass 3 through the variants
    178 20:51:01.497 INFO  FilterMutectCalls - Finished pass 3 through the variants
    179 20:51:01.504 INFO  FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
    180 20:51:01.505 INFO  FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter 
    181 
    182 20:51:01.505 INFO  ProgressMeter -             unmapped              0.0                    16           6233.8
    183 20:51:01.505 INFO  ProgressMeter - Traversal complete. Processed 16 total variants in 0.0 minutes.
    184 20:51:01.510 INFO  FilterMutectCalls - Shutting down engine
    185 [November 19, 2024 at 8:51:01 PM KST] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.01 minutes.
    186 Runtime.totalMemory()=285212672
    187 Completed FilterMutect2 run

best regards,

Seungho Oh