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Use when joint-genotyping one or more germline gVCFs into a cohort VCF with GATK GenotypeGVCFs.
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Based on SOC occupation classification
Use when running GATK HaplotypeCaller to emit per-sample germline variant calls or gVCFs from analysis-ready BAM/CRAM inputs.
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-genotypegvcfs |
| description | Use when joint-genotyping one or more germline gVCFs into a cohort VCF with GATK GenotypeGVCFs. |
| disable-model-invocation | true |
| user-invocable | true |
gatk GenotypeGVCFs/home/vimalinx/miniforge3/envs/bio/bin/gatkgatk executable on PATH.gatk GenotypeGVCFs \
-R reference.fa \
-V cohort.g.vcf.gz \
-O cohort.joint.vcf.gz
gatk executable still has to exist for real execution.