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Use when running GATK HaplotypeCaller to emit per-sample germline variant calls or gVCFs from analysis-ready BAM/CRAM inputs.
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Based on SOC occupation classification
Use when joint-genotyping one or more germline gVCFs into a cohort VCF with GATK GenotypeGVCFs.
Use when splitting mixed accession-like text into one lowercase token per line in EDirect-style text pipelines.
Use when converting ACE assembly files into SAM while preserving legacy ACE-specific padded or contig-sequence behavior.
Use when pretty-printing tab-delimited output with left, center, right, or decimal-aware numeric alignment in EDirect text workflows.
Use when masking columns or coordinate ranges in multiple-sequence alignments before downstream HMMER or alignment-processing steps.
Use when counting amino-acid letters in raw protein sequence lines inside simple EDirect text pipelines.
| name | gatk-haplotypecaller |
| description | Use when running GATK HaplotypeCaller to emit per-sample germline variant calls or gVCFs from analysis-ready BAM/CRAM inputs. |
| disable-model-invocation | true |
| user-invocable | true |
gatk HaplotypeCaller/home/vimalinx/miniforge3/envs/bio/bin/gatkgatk executable on PATH.gatk HaplotypeCaller \
-R reference.fa \
-I sample.analysis_ready.bam \
-O sample.g.vcf.gz \
-ERC GVCF
-ERC GVCF, not a raw single-sample VCF.gatk executable still has to exist for real execution.