GATK4 -Call somatic SNVs and INDELs with Mutect2

Description

Call somatic short variants via local assembly of haplotypes. Short variants include single nucleotide (SNV) and insertion and deletion (indel) variants.

Parameters

Details

Call somatic short variants via local assembly of haplotypes. Short variants include single nucleotide (SNV) and insertion and deletion (indel) variants. The caller combines the DREAM challenge-winning somatic genotyping engine of the original MuTect (Cibulskis et al., 2013) with the assembly-based machinery of HaplotypeCaller.

Based on GATK4 Mutect2 tool. For more detailed information, see GATK documentation,

Output

References

This tool is based on the GATK4 package.

For instructions on citing GATK4, please see GATK FAQ