Function
GATK HaplotypeCaller identifies SNPs and indels by performing local de novo assembly
of haplotypes in active genomic regions and then assigns genotypes based on read evidence.
Input Format
- Reference Genome (
.fa, .fasta)
- BAM File (
.bam)
- Optional VCF (Known Sites)
- Optional Interval List
- Read Group metadata (RGID, RGLB, RGPL, RGPU, RGSM)
Output Format
- VCF or GVCF file containing SNP and Indel calls
- Variant quality annotations and genotype fields
Example Usage
gatk HaplotypeCaller -R ref.fa -I input.bam -O output.vcf
gatk HaplotypeCaller -R ref.fa -I input.bam -O sample.g.vcf.gz -ERC GVCF
gatk HaplotypeCaller -R ref.fa -I input.bam -O output.vcf \
-L intervals.bed --sample-ploidy 2
Applications
- SNP and Indel discovery
- Clinical variant calling
- Population genomics studies
- Joint genotyping workflows
- Targeted sequencing analysis
Suggested Reading
Important Notes:
- Reference FASTA must be indexed (.fai + .dict).
- BAM must be sorted, indexed, and contain read groups.
- GVCF mode is recommended for multi-sample analysis.
- Missing read groups are a common cause of failure.
