Call somatic SNVs and indels via local assembly of haplotypes
In data directory, tool searches for the following in this specific path structure,
-
Alignment
- Normal
- normal.bam
- if indexes (optional) are not provided, the tool will create them for you.
- Tumor
- tumor.bam
- Normal
-
Reference
- hg38.fa
- hg38.fa.fai
-
Germline
- af-only.gnomad.hg38.vcf.gz
- af-only-gnomad.hg38.vcf.gz.tbi
-
Panel of Normals
- 1000g_pon.hg38.vcf.gz
- 1000g_pon.hg38.vcf.gz.tbi
Folder name reflects which comparison was done.
- normal_tumor
- .vcf.gz: somatic variants
- .vcf.gz.stats: somatic variants stats
- .vcf.gz.tbi: somatic variants index
https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2
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