**Confirm the heap GATK actually started with.** Check the GATK log header for the Java command line and the max heap value. Expected: the log shows a small default heap, often far below the memory free on the machine.

**Rerun with an explicit larger heap.** Add the java options setting to the HaplotypeCaller command, for example a heap of 8 gigabytes on a machine that has that memory free, keeping the rest of the command unchanged. Success check: the log header now shows the larger max heap you set.

**Test on one small interval first.** Run the same command limited to a single short interval or a small chromosome region. Expected: the test run finishes and writes a valid VCF instead of ending with OutOfMemoryError.

**Split large jobs by interval.** If whole genome runs still exhaust a reasonable heap, run HaplotypeCaller per interval in parallel and merge the resulting VCF files afterwards. Success check: each interval job completes on its own heap and the merged VCF contains records from every interval.

**Check for an oversized input problem.** Look for an unindexed BAM, a BAM with an unusually deep region, or a missing interval list that makes the tool load more than intended. Expected: the input BAM has an index file beside it and the run is scoped to the intended genome.

---

## Vectle citations

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## Selected public attribution and original notices/references

```json
{
  "author": "Fin",
  "client": null,
  "notices_and_references": []
}
```