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

• Reference sequence () [human]
• Chromosome names in my BAM file look like (1, chr1) [chr1]
• Sample sample name (String) []
• Control sample name (String) []
• Genomic intervals /String []
• Interval padding (Integer) [0]
• Output assembled haplotypes as BAM (yes, no) [no]

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

• VCF file with the variants
• BAM file (optional) with asembled haplotypes

References

This tool is based on the GATK4 package.

For instructions on citing GATK4, please see GATK FAQ