> This page is for version v4.8.0 (default). > For other versions, use one of these documentation indexes: > - v4.8.0 (default): https://docs.nvidia.com/clara/parabricks/v4.8.0/llms.txt > - v4.7.1: https://docs.nvidia.com/clara/parabricks/v4.7.1/llms.txt > For clean Markdown of any page, append .md to the page URL. > For a complete documentation index, see https://docs.nvidia.com/clara/parabricks/llms.txt. > For AI client integration (Claude Code, Cursor, etc.), connect to the MCP server at https://docs.nvidia.com/clara/parabricks/_mcp/server. # haplotypecaller This tool is an accelerated version of the GATK germline variant caller, HaplotypeCaller, which takes an aligned BAM/CRAM file (for example, from the fq2bam tool), and outputs a VCF file. It calls germline SNPs and indels via local re-assembly of haplotypes: whenever it encounters a region showing signs of variation, it discards the existing mapping information and completely reassembles the reads in that region, making it more accurate when calling regions that are traditionally difficult to call. You can optionally provide a BQSR report using the `--in-recal-file` option to fix the BAM, similar to ApplyBQSR. In this case, the updated base qualities will be used. This report is not required; provide it only if you have previously generated one by running `pbrun bqsr`. ![](/clara/parabricks/_fern-files/parabricks-clara.docs.buildwithfern.com/e5b513f82eee37f6054b72e62773f39b4e68f85c372053e9071e3907e93ab520/assets/images/parabricks-web-graphics-1259949-r2-haplotypecaller.svg) Refer to the [haplotypecaller Reference](#options) section for a detailed listing of all available options. ## Quick Start ```sh # This command assumes all the inputs are in the current working directory and all the outputs go to the same place. docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \ --workdir /workdir \ nvcr.io/nvidia/clara/clara-parabricks:4.8.0-1 \ pbrun haplotypecaller \ --ref /workdir/${REFERENCE_FILE} \ --in-bam /workdir/${INPUT_BAM_FILE} \ --out-variants /outputdir/${OUTPUT_VCF_FILE} ``` ## Compatible GATK4 Command The commands below are the GATK4 counterpart of the Parabricks command above. The output from these commands will be functionally equivalent to the output from the above command; see the Source of Mismatches section below for known small differences. The ApplyBQSR step corresponds to the optional `--in-recal-file` input of `pbrun haplotypecaller`, which the Quick Start above omits because the BQSR report is optional. Refer to the [Output Comparison](/clara/parabricks/v4.8.0/about-parabricks/comparison-with-baseline-tools) page for comparing the results. ```sh # Run ApplyBQSR Step $ gatk ApplyBQSR \ --java-options -Xmx30g \ -R Ref/Homo_sapiens_assembly38.fasta \ -I mark_dups_cpu.bam \ --bqsr-recal-file recal_file.txt \ -O cpu_nodups_BQSR.bam #Run Haplotype Caller $ gatk HaplotypeCaller \ --java-options -Xmx30g \ --input cpu_nodups_BQSR.bam \ --output result_cpu.vcf \ --reference Ref/Homo_sapiens_assembly38.fasta \ --native-pair-hmm-threads 16 ``` ## Source of Mismatches While the Parabricks HaplotypeCaller does not lose any accuracy in functionality when compared with the GATK HaplotypeCaller there are a few implementation differences that can result in slightly different output files. * **Random generator** The GATK HaplotypeCaller calls the same random generator in read downsampling and **QualByDepth** annotation computation. The Parabricks HaplotypeCaller calls two separate random number generators to allow for parallel computing. * **Log10 implementation** The `log10` operation is used to compute the haplotype penalty score. The Java implementation `java.lang.Math.log10()` is slightly different from the C++ `cmath` library, giving rise to small mismatches in computed scores. Different haplotypes might be selected because of this. * **AVX** GATK calls Intel GKL (Genomics Kernel Library) which contains optimized versions of compute kernels (e.g. Smith-Waterman, PairHMM) to run on Intel Architecture (AVX, AVX2, AVX-512, and multicore). However, some SIMD intrinsics such as `_mm512_mul_ps` can generate a slightly different output when compared with the serial operations which our GPU implementation is based on. * **HashMap, HashSet iteration** GATK can give non-deterministic outputs because iterating over a Java `HashMap` or `HashSet` does not preserve order. Parabricks always gives deterministic output by using a hash table that preserves the insertion order (similar to `LinkedHashMap` in Java). Several original HaplotypeCaller options are supported by Parabricks. To specify the inclusion or exclusion of several haplotype caller annotations, use the `--haplotypecaller-options` option: ```sh $ docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \ --workdir /workdir \ nvcr.io/nvidia/clara/clara-parabricks:4.8.0-1 \ pbrun haplotypecaller \ ... --haplotypecaller-options '-min-pruning 4 -A AS_BaseQualityRankSumTest -A TandemRepeat' ... ``` Annotations may be excluded in the same manner using the `-AX` option. There should be a space between the `-A`/`-AX` flag and its value. The following are supported options and their allowed values: * -A * AS_BaseQualityRankSumTest * AS_FisherStrand * AS_InbreedingCoeff * AS_MappingQualityRankSumTest * AS_QualByDepth * AS_RMSMappingQuality * AS_ReadPosRankSumTest * AS_StrandOddsRatio * AssemblyComplexity * BaseQualityRankSumTest * ChromosomeCounts * ClippingRankSumTest * Coverage * DepthPerAlleleBySample * DepthPerSampleHC * ExcessHet * FisherStrand * InbreedingCoeff * MappingQualityRankSumTest * QualByDepth * RMSMappingQuality * ReadPosRankSumTest * ReferenceBases * StrandBiasBySample * StrandOddsRatio * TandemRepeat * -AX * (same as for the *-A* option) * \--output-mode * EMIT_VARIANTS_ONLY * EMIT_ALL_CONFIDENT_SITES * EMIT_ALL_ACTIVE_SITES * -max-reads-per-alignment-start * a positive integer * -min-dangling-branch-length * a positive integer * -min-pruning * a positive integer * -pcr-indel-model * NONE * HOSTILE * AGGRESSIVE * CONSERVATIVE * -standard-min-confidence-threshold-for-calling * a positive integer ## Options | Type | Name | Required? | Description | | ----------- | ------------------------------------------------------------------------------------- | --------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | I/O | `--ref REF` | Yes | Path to the reference file. | | I/O | `--in-bam IN_BAM` | Yes | Path to the input BAM/CRAM file for variant calling. The argument may also be a local folder containing several BAM files. | | I/O | `--in-recal-file IN_RECAL_FILE` | No | Path to the input BQSR report. | | I/O | `--interval-file INTERVAL_FILE` | No | Path to an interval file in one of these formats: Picard-style (.interval_list or .picard), GATK-style (.list or .intervals), or BED file (.bed). This option can be used multiple times. | | I/O | `--htvc-bam-output HTVC_BAM_OUTPUT` | No | File to which assembled haplotypes should be written. If passing with --run-partition, multiple BAM files will be written. | | I/O | `--out-variants OUT_VARIANTS` | Yes | Path of the vcf/vcf.gz/g.vcf/gvcf.gz file after variant calling. | | I/O | `--htvc-alleles HTVC_ALLELES` | No | Path of the vcf.gz force-call file. The set of alleles to force-call regardless of evidence. | | Tool | `--haplotypecaller-options HAPLOTYPECALLER_OPTIONS` | No | Pass supported haplotype caller options as one string. The following are currently supported original haplotypecaller options: -A \,-AX \,--output-mode \ ,-max-reads-per-alignment-start \, -min-dangling-branch-length \, -min-pruning \, -pcr-indel-model \, -standard-min-confidence-threshold-for-calling \, --activeregion-alt-multiplier \(e.g. --haplotypecaller-options="-min-pruning 4 -standard-min-confidence-threshold-for-calling 30"). Allele-specific annotations (names starting with AS\_) require --gvcf. | | Tool | `--static-quantized-quals STATIC_QUANTIZED_QUALS` | No | Use static quantized quality scores to a given number of levels. Repeat this option multiple times for multiple bins. | | Tool | `--gvcf` | No | Generate variant calls in .gvcf format. | | Tool | `--disable-read-filter DISABLE_READ_FILTER` | No | Disable the read filters for BAM entries. Currently, the supported read filters that can be disabled are MappingQualityAvailableReadFilter, MappingQualityReadFilter, NotSecondaryAlignmentReadFilter, and WellformedReadFilter. | | Tool | `--max-alternate-alleles MAX_ALTERNATE_ALLELES` | No | Maximum number of alternate alleles to genotype. | | Tool | `-G ANNOTATION_GROUP, --annotation-group ANNOTATION_GROUP` | No | The groups of annotations to add to the output variant calls. Currently supported annotation groups are StandardAnnotation, StandardHCAnnotation, and AS_StandardAnnotation. AS_StandardAnnotation requires --gvcf. | | Tool | `-GQB GVCF_GQ_BANDS, --gvcf-gq-bands GVCF_GQ_BANDS` | No | Exclusive upper bounds for reference confidence GQ bands. Must be in the range \[1, 100] and specified in increasing order. | | Tool | `--rna` | No | Run haplotypecaller optimized for RNA data. | | Tool | `--dont-use-soft-clipped-bases` | No | Don't use soft clipped bases for variant calling. | | Tool | `--minimum-mapping-quality MINIMUM_MAPPING_QUALITY` | No | Minimum mapping quality to keep (inclusive). | | Tool | `--mapping-quality-threshold-for-genotyping MAPPING_QUALITY_THRESHOLD_FOR_GENOTYPING` | No | Control the threshold for discounting reads from the genotyper due to mapping quality after the active region detection and assembly steps but before genotyping. | | Tool | `--enable-dynamic-read-disqualification-for-genotyping` | No | Will enable less strict read disqualification low base quality reads. | | Tool | `--min-base-quality-score MIN_BASE_QUALITY_SCORE` | No | Minimum base quality required to consider a base for calling. | | Tool | `--adaptive-pruning` | No | Use adaptive graph pruning algorithm when pruning De Bruijn graph. | | Tool | `--force-call-filtered-alleles` | No | Force-call filtered alleles included in the resource specified by --alleles. | | Tool | `--filter-reads-too-long` | No | Ignore all input BAM reads with size > 500bp. | | Tool | `--no-alt-contigs` | No | Get rid of output records for alternate contigs. | | Tool | `--ploidy PLOIDY` | No | Ploidy assumed for the BAM file. Currently only haploid (ploidy 1) and diploid (ploidy 2) are supported. (default: 2) | | Tool | `-L INTERVAL, --interval INTERVAL` | No | Interval within which to call the variants from the BAM/CRAM file. All intervals will have a padding of 100 to get read records, and overlapping intervals will be combined. Interval files should be passed using the --interval-file option. This option can be used multiple times (e.g. "-L chr1 -L chr2:10000 -L chr3:20000+ -L chr4:10000-20000"). | | Tool | `-XL EXCLUDE_INTERVALS, --exclude-intervals EXCLUDE_INTERVALS` | No | Genomic intervals to exclude from processing. Use the same format as --interval option. Excluded intervals are subtracted from the include intervals. This option can be used multiple times (e.g. "-XL chr1:1000-2000 -XL chr2:5000-6000"). | | Tool | `-ip INTERVAL_PADDING, --interval-padding INTERVAL_PADDING` | No | Amount of padding (in base pairs) to add to each interval you are including. | | Performance | `--htvc-low-memory` | No | Use low memory mode in htvc. | | Performance | `--num-htvc-threads NUM_HTVC_THREADS` | No | Number of CPU threads per GPU to use. (default: 5) | | Performance | `--num-streams-per-gpu NUM_STREAMS_PER_GPU` | No | Number of streams (pipelines) to use per GPU. Default is 'auto', which selects an optimal count based on GPU memory, GPU count, and partition mode. Pass a positive integer to override. (default: auto) | | Performance | `--run-partition` | No | Divide the whole genome into multiple partitions and run multiple processes at the same time, each on one partition. | | Performance | `--gpu-num-per-partition GPU_NUM_PER_PARTITION` | No | Number of GPUs to use per partition. | | Runtime | `--verbose` | No | Enable verbose output. | | Runtime | `--x3` | No | Show full command line arguments. | | Runtime | `--dry-run` | No | Check if the current command is valid. | | Runtime | `--logfile LOGFILE` | No | Path to the log file. If not specified, messages will only be written to the standard error output. | | Runtime | `--tmp-dir TMP_DIR` | No | Full path to the directory where temporary files will be stored. (default: .) | | Runtime | `--with-petagene-dir WITH_PETAGENE_DIR` | No | Full path to the PetaGene installation directory. By default, this should have been installed at /opt/petagene. Use of this option also requires that the PetaLink library has been preloaded by setting the LD_PRELOAD environment variable. Optionally set the PETASUITE_REFPATH and PGCLOUD_CREDPATH environment variables that are used for data and credentials. Optionally set the PetaLinkMode environment variable that is used to further configure PetaLink, notably setting it to "+write" to enable outputting compressed BAM and .fastq files. | | Runtime | `--keep-tmp` | No | Do not delete the directory storing temporary files after completion. | | Runtime | `--no-seccomp-override` | No | Do not override seccomp options for docker. | | Runtime | `--version` | No | View compatible software versions. | | Runtime | `--preserve-file-symlinks` | No | Override default behavior to keep file symlinks intact and *not* resolve the symlink. | | Runtime | `--help-json` | No | Print out help message in JSON format. | | Runtime | `--num-gpus NUM_GPUS` | No | Number of GPUs to use for a run. (default: 1) | > **Note** > > The `--run-partition` option splits the run into partitions, each using > `--gpu-num-per-partition` GPUs (default 2). `--num-gpus` must be a multiple of > `--gpu-num-per-partition`, so at least 2 GPUs are required; running with `--num-gpus 1` > will cause the tool to exit with an error. > **Note** > > In the values provided to *--haplotypecaller-options* --output-mode requires two leading hyphens, while all other values take a single hyphen.