haplotypecaller

Run a GPU-accelerated haplotypecaller.

This tool applies an accelerated GATK CollectMultipleMetrics for assessing the metrics of a BAM file, such as including alignment success, quality score distributions, GC bias, and sequencing artifacts. This functions as a ‘meta-metrics’ tool, and can run any combination of the available metrics tools in GATK to assess overall how well a sequencing run has performed. The available metrics tools (PROGRAMs) can be found in the command line example below.

You can provide an optional BQSR report to fix the BAM, similar to ApplyBQSR. In this case, the updated base qualities will be used.

Quick Start

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            # This command assumes all the inputs are in INPUT_DIR and all the outputs go to OUTPUT_DIR.
docker run --rm --gpus all --volume INPUT_DIR:/workdir --volume OUTPUT_DIR:/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.2.1-1 \
    pbrun haplotypecaller \
    --ref /workdir/${REFERENCE_FILE} \
    --in-bam /workdir/${INPUT_BAM} \
    --in-recal-file /workdir/${INPUT_RECAL_FILE} \
    --out-variants /outputdir/${OUTPUT_VCF}

Compatible GATK4 Command

The commands below are the GATK4 counterpart of the Parabricks command above. The output from these commands will be identical to the output from the above command. See the Output Comparison page for comparing the results.

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            # 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

Specifying Haplotype Caller options

Several original HaplotypeCaller options are supported by Parabricks. To specify the inclusion or exclusion of several haplotype caller annotations, use the --haplotypecaller-options option:

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            $ # This command assumes all the inputs are in INPUT_DIR and all the outputs go to OUTPUT_DIR.
docker run --rm --gpus all --volume INPUT_DIR:/workdir --volume OUTPUT_DIR:/outputdir \
     --workdir /workdir \
     nvcr.io/nvidia/clara/clara-parabricks:4.2.1-1 \
     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
- 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

haplotypecaller Reference

Run HaplotypeCaller to convert BAM/CRAM to VCF.

Input/Output file options

--ref REF
--in-bam IN_BAM
--in-recal-file IN_RECAL_FILE
--interval-file INTERVAL_FILE
--htvc-bam-output HTVC_BAM_OUTPUT
--out-variants OUT_VARIANTS

Tool Options:

--haplotypecaller-options HAPLOTYPECALLER_OPTIONS
--static-quantized-quals STATIC_QUANTIZED_QUALS
--gvcf
--disable-read-filter DISABLE_READ_FILTER
--max-alternate-alleles MAX_ALTERNATE_ALLELES
-G ANNOTATION_GROUP, --annotation-group ANNOTATION_GROUP
-GQB GVCF_GQ_BANDS, --gvcf-gq-bands GVCF_GQ_BANDS
--rna
--dont-use-soft-clipped-bases
--no-alt-contigs
--ploidy PLOIDY
-L INTERVAL, --interval INTERVAL
-ip INTERVAL_PADDING, --interval-padding INTERVAL_PADDING
--sample-sex SAMPLE_SEX
--range-male RANGE_MALE
--range-female RANGE_FEMALE
--use-GRCh37-regions

Performance Options:

--htvc-low-memory
--num-htvc-threads NUM_HTVC_THREADS
--run-partition

Common options:

--logfile LOGFILE
--tmp-dir TMP_DIR
--with-petagene-dir WITH_PETAGENE_DIR
--keep-tmp
--no-seccomp-override
--version

GPU options:

--num-gpus NUM_GPUS

Note

In the values provided to --haplotypecaller-options --output-mode requires two leading hyphens, while all other values take a single hyphen.