When I run GetPileupSummaries with a small example bam, all the output columns are zero, even though I know that the bam contains a read that overlaps the variants. This seems to be the same issue as in these two tickets:

https://gatk.broadinstitute.org/hc/en-us/community/posts/19788847161755-GetPileupSummaries-output-all-0?input_string=GetPileupSummaries%20all

https://gatk.broadinstitute.org/hc/en-us/community/posts/360076863391-Question-GetPileupSummaries-columns-all-0?input_string=GetPileupSummaries%20all

But neither of those issues were resolved.

a) GATK version used:

The Genome Analysis Toolkit (GATK) v4.5.0.0
Java runtime: OpenJDK 64-Bit Server VM v21.0.2+13-LTS

b) Exact command used:

gatk GetPileupSummaries --input test.bam --variant small_exac_common_3.hg38.vcf.gz --output test.table --reference chr1.fa -max-af 0.3 --intervals test.bed

c) Entire program log:

Using GATK jar /Users/Steven.Strong/Downloads/gatk-4.5.0.0/gatk-package-4.5.0.0-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 -jar /Users/Steven.Strong/Downloads/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar GetPileupSummaries --input test.bam --variant small_exac_common_3.hg38.vcf.gz --output test.table --reference chr1.fa -max-af 0.3 --intervals test.bed
14:05:24.839 INFO  NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/Steven.Strong/Downloads/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib
14:05:24.862 WARN  NativeLibraryLoader - Unable to load libgkl_compression.dylib from native/libgkl_compression.dylib (/private/var/folders/5p/6168bwcn7lzcjvzl3kdkc52h0000gp/T/libgkl_compression16741880035170389975.dylib: dlopen(/private/var/folders/5p/6168bwcn7lzcjvzl3kdkc52h0000gp/T/libgkl_compression16741880035170389975.dylib, 0x0001): tried: '/private/var/folders/5p/6168bwcn7lzcjvzl3kdkc52h0000gp/T/libgkl_compression16741880035170389975.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/private/var/folders/5p/6168bwcn7lzcjvzl3kdkc52h0000gp/T/libgkl_compression16741880035170389975.dylib' (no such file), '/private/var/folders/5p/6168bwcn7lzcjvzl3kdkc52h0000gp/T/libgkl_compression16741880035170389975.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64')))
14:05:24.864 INFO  NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/Steven.Strong/Downloads/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib
14:05:24.866 WARN  NativeLibraryLoader - Unable to load libgkl_compression.dylib from native/libgkl_compression.dylib (/private/var/folders/5p/6168bwcn7lzcjvzl3kdkc52h0000gp/T/libgkl_compression1128659698013723509.dylib: dlopen(/private/var/folders/5p/6168bwcn7lzcjvzl3kdkc52h0000gp/T/libgkl_compression1128659698013723509.dylib, 0x0001): tried: '/private/var/folders/5p/6168bwcn7lzcjvzl3kdkc52h0000gp/T/libgkl_compression1128659698013723509.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/private/var/folders/5p/6168bwcn7lzcjvzl3kdkc52h0000gp/T/libgkl_compression1128659698013723509.dylib' (no such file), '/private/var/folders/5p/6168bwcn7lzcjvzl3kdkc52h0000gp/T/libgkl_compression1128659698013723509.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64')))
14:05:24.927 INFO  GetPileupSummaries - ------------------------------------------------------------
14:05:24.929 INFO  GetPileupSummaries - The Genome Analysis Toolkit (GATK) v4.5.0.0
14:05:24.929 INFO  GetPileupSummaries - For support and documentation go to https://software.broadinstitute.org/gatk/
14:05:24.930 INFO  GetPileupSummaries - Executing as Steven.Strong@MacBook-Pro-K7T94FCQK2.local on Mac OS X v14.4.1 aarch64
14:05:24.930 INFO  GetPileupSummaries - Java runtime: OpenJDK 64-Bit Server VM v21.0.2+13-LTS
14:05:24.930 INFO  GetPileupSummaries - Start Date/Time: April 15, 2024, 2:05:24 PM MDT
14:05:24.930 INFO  GetPileupSummaries - ------------------------------------------------------------
14:05:24.930 INFO  GetPileupSummaries - ------------------------------------------------------------
14:05:24.930 INFO  GetPileupSummaries - HTSJDK Version: 4.1.0
14:05:24.930 INFO  GetPileupSummaries - Picard Version: 3.1.1
14:05:24.931 INFO  GetPileupSummaries - Built for Spark Version: 3.5.0
14:05:24.931 INFO  GetPileupSummaries - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:05:24.931 INFO  GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:05:24.931 INFO  GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:05:24.931 INFO  GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:05:24.931 INFO  GetPileupSummaries - Deflater: JdkDeflater
14:05:24.931 INFO  GetPileupSummaries - Inflater: JdkInflater
14:05:24.931 INFO  GetPileupSummaries - GCS max retries/reopens: 20
14:05:24.931 INFO  GetPileupSummaries - Requester pays: disabled
14:05:24.931 INFO  GetPileupSummaries - Initializing engine
14:05:24.954 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
14:05:24.955 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
14:05:25.003 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
14:05:25.010 INFO  FeatureManager - Using codec VCFCodec to read file file:///Users/Steven.Strong/Desktop/small_exac_common_3.hg38.vcf.gz
14:05:25.016 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
14:05:25.016 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
14:05:25.036 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
14:05:25.063 INFO  FeatureManager - Using codec BEDCodec to read file file:///Users/Steven.Strong/Desktop/test.bed
14:05:25.064 INFO  IntervalArgumentCollection - Processing 2999997 bp from intervals
14:05:25.075 INFO  GetPileupSummaries - Done initializing engine
14:05:25.078 INFO  ProgressMeter - Starting traversal
14:05:25.078 INFO  ProgressMeter -        Current Locus  Elapsed Minutes        Loci Processed      Loci/Minute
14:05:25.104 INFO  GetPileupSummaries - 0 read(s) filtered by: MappingQualityAvailableReadFilter 
0 read(s) filtered by: MappingQualityNotZeroReadFilter 
0 read(s) filtered by: MappedReadFilter 
0 read(s) filtered by: PrimaryLineReadFilter 
0 read(s) filtered by: NotDuplicateReadFilter 
0 read(s) filtered by: PassesVendorQualityCheckReadFilter 
0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter 
0 read(s) filtered by: MateOnSameContigOrNoMappedMateReadFilter 
0 read(s) filtered by: GoodCigarReadFilter 
0 read(s) filtered by: WellformedReadFilter 
0 total reads filtered out of 2 reads processed
14:05:25.104 INFO  ProgressMeter -             unmapped              0.0                   182         420000.0
14:05:25.104 INFO  ProgressMeter - Traversal complete. Processed 182 total loci in 0.0 minutes.
14:05:25.104 INFO  GetPileupSummaries - Shutting down engine
[April 15, 2024, 2:05:25 PM MDT] org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=327155712
Tool returned:
SUCCESS

The reference is

s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/Chromosomes/chr1.fa

The bam looks like this

$ samtools view -h test.bam
@HD    VN:1.6    SO:coordinate
@SQ    SN:chr1    LN:248956422    M5:6aef897c3d6ff0c78aff06ac189178dd
@RG    ID:7dc37610-761d-4b61-b054-f2cf7a252e47    SM:7dc37610-761d-4b61-b054-f2cf7a252e47    PL:ILLUMINA
@PG    ID:samtools    PN:samtools    VN:1.19.2    CL:samtools view -h -o test.bam
@PG    ID:samtools.1    PN:samtools    PP:samtools    VN:1.19.2    CL:samtools view -h test.bam
A00827:893:HM2TFDSX7:4:2149:1380:31156:GATCT-GTAGT    163    chr1    139099    1    96M    =    139185    182    GGCCAGTGTGAGGCAAGACCTGGGCCTGTCTAGGCTGCTGGGAGACAGGCAGGAATCTGGCCAGGGAAGGTTGCCATGAGACAAAAGTTGGGCCTG    FFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:,FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFF    XG:i:0    XM:i:0    XN:i:0    XO:i:0    AS:i:0    XS:i:0    YS:i:-10    YT:Z:CP    cr:i:0    cf:i:0    gf:f:58.791gr:f:60.4167    oe:f:0    ab:i:1    qm:f:37    qn:f:37    PG:Z:MarkDuplicates    RG:Z:7dc37610-761d-4b61-b054-f2cf7a252e47    MD:Z:96    NM:i:0
A00827:893:HM2TFDSX7:4:2149:1380:31156:GATCT-GTAGT    83    chr1    139185    1    96M    =    139099    -182    GTTGGGCCTGGAAAGGCCCTTGTGAAGCGTGAGCTTGGCCTAAAGAGGACACTGGGTGGCAGGAGCTGGGTGTGTAGAAGCTGCTGAAAGGTTGGG    FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF    XG:i:0    XM:i:2    XN:i:0    XO:i:0    AS:i:-10    XS:i:-10    YS:i:0    YT:Z:CP    cr:i:1    cf:i:0    gf:f:58.7912    gr:f:58.3333    oe:f:0    ab:i:1    qm:f:37    qn:f:37    PG:Z:MarkDuplicates    RG:Z:7dc37610-761d-4b61-b054-f2cf7a252e47    MD:Z:28A19C47    NM:i:2

the intervals file is

$ cat test.bed
chr1    3    3000000

the output is:

$ cat test.table
#<METADATA>SAMPLE=7dc37610-761d-4b61-b054-f2cf7a252e47
contig    position    ref_count    alt_count    other_alt_count    allele_frequency
chr1    139213    0    0    0    0.233
chr1    139233    0    0    0    0.231

I tried running gatk ValidateSamFile and I get no errors