القائمة
Use when running GATK HaplotypeCaller to emit per-sample germline variant calls or gVCFs from analysis-ready BAM/CRAM inputs.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
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.