REQUIRED for all errors and issues:
a) GATK version used:
4.1.9.0
 
b) Exact command used:
b-1) With -ERC GVCF:
##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --sample-ploidy 2 --gvcf-gq-bands 10 --gvcf-gq-bands 20 --gvcf-gq-bands 30 --gvcf-gq-bands 40 --gvcf-gq-bands 60 --gvcf-gq-bands 80 --native-pair-hmm-threads 1 --emit-ref-confidence GVCF --output /storm/Analysis/Genome_Health/24GHP021/GHP/work/bcbiotx/tmpcxuqxrha/24GHP021-121_20220120-171-0014-joint-chr1_0_18097745.vcf.gz --intervals /storm/Analysis/Genome_Health/24GHP021/GHP/work/gatk-haplotype/chr1/24GHP021-121_20220120-171-0014-joint-chr1_0_18097745-regions.bed --interval-set-rule INTERSECTION --input /storm/Analysis/Genome_Health/24GHP021/GHP/work/align/24GHP021-121_20220120-171-0014/24GHP021-121_20220120-171-0014-sort-recal.bam --reference /storm/Tools/bcbio/bcbio_v1.2.4/genomes/Hsapiens/hg19_nocontig/seq/hg19_nocontig.fa --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation MappingQuality --annotation DepthPerAlleleBySample --annotation Coverage --annotation ClippingRankSumTest --annotation DepthPerSampleHC --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --num-reference-samples-if-no-call 0 --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --floor-blocks false --indel-size-to-eliminate-in-ref-model 10 --disable-optimizations false --just-determine-active-regions false --dont-genotype false --do-not-run-physical-phasing false --do-not-correct-overlapping-quality false --use-filtered-reads-for-annotations false --adaptive-pruning false --do-not-recover-dangling-branches false --recover-dangling-heads false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --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-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --max-mnp-distance 0 --force-call-filtered-alleles false --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-reads-per-alignment-start 50 --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 --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false --allow-old-rms-mapping-quality-annotation-data false",Version="4.1.9.0",Date="February 8, 2024 5:03:19 AM KST">

b-2) With -ERC BP_RESOLUTION:
##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --sample-ploidy 2 --gvcf-gq-bands 10 --gvcf-gq-bands 20 --gvcf-gq-bands 30 --gvcf-gq-bands 40 --gvcf-gq-bands 60 --gvcf-gq-bands 80 --native-pair-hmm-threads 1 --emit-ref-confidence BP_RESOLUTION --output /storm/Analysis/Genome_Health/24GHP021/vcf/24GHP021-121_20220120-171-0014-joint.vcf.gz --intervals /storm/Analysis/Genome_Health/Script/bed/GHP.v2_target_300bp_4delSNV.bed --interval-set-rule INTERSECTION --input /storm/Analysis/Genome_Health/24GHP021/GHP/work/align/24GHP021-121_20220120-171-0014/24GHP021-121_20220120-171-0014-sort.bam --reference /storm/Tools/bcbio/bcbio_v1.2.4/genomes/Hsapiens/hg19_nocontig/seq/hg19_nocontig.fa --tmp-dir /storm/Analysis/Genome_Health/24GHP021/GHP/work/bcbiotx/tmp --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation MappingQuality --annotation DepthPerAlleleBySample --annotation Coverage --annotation ClippingRankSumTest --annotation DepthPerSampleHC --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --num-reference-samples-if-no-call 0 --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --floor-blocks false --indel-size-to-eliminate-in-ref-model 10 --disable-optimizations false --just-determine-active-regions false --dont-genotype false --do-not-run-physical-phasing false --do-not-correct-overlapping-quality false --use-filtered-reads-for-annotations false --adaptive-pruning false --do-not-recover-dangling-branches false --recover-dangling-heads false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --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-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --max-mnp-distance 0 --force-call-filtered-alleles false --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-reads-per-alignment-start 50 --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 --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false --allow-old-rms-mapping-quality-annotation-data false",Version="4.1.9.0",Date="February 15, 2024 3:21:49 PM KST">
c) Entire program log:

I created a GVCF using HaplotypeCaller because I wanted to check the variant information in the region chr7:142458451. Here's what I found:

1) With -ERC GVCF:
In this case, the information for the region chr7:142458451 does not appear:
```
chr7    142458151       .       C       <NON_REF>       .       .       END=142458403   GT:DP:GQ:MIN_DP:PL      0/0:1:0:0:0,0,0
chr7    142458699       .       C       <NON_REF>       .       .       END=142458751   GT:DP:GQ:MIN_DP:PL      0/0:0:0:0:0,0,0
```

2) With -ERC BP_RESOLUTION:
In this case, the information for the region chr7:142458451 is present:
```
chr7    142458450       .       A       <NON_REF>       .       .       .       GT:AD:DP:GQ:PL  0/0:2,0:2:6:0,6,84
chr7    142458451       .       A       <NON_REF>       .       .       .       GT:AD:DP:GQ:PL  0/0:2,0:2:6:0,6,84
chr7    142458452       .       C       <NON_REF>       .       .       .       GT:AD:DP:GQ:PL  0/0:2,0:2:6:0,6,84
```

When using GenotypeGVCFs with the --include-non-variant-sites option:
1) The region chr7:142458451 information is missing in the output from case 1).
2) The region chr7:142458451 information is present only in the output from case 2), as shown below:
```
chr7    142458451       .       A       .       .       .       DP=2    GT:AD:DP:RGQ    0/0:2:2:6
```

The difference in results between -ERC GVCF and -ERC BP_RESOLUTION in the GVCF creation is typically attributed to the file size and the granularity of representation in base units. However, in this case, the presence or absence of information for the region chr7:142458451 in the GVCF file results in different outputs in the VCF file. Could you please explain why this is happening?