Recently published apps
- GATK Somatic SNVs and INDELs (Mutect2) 22.214.171.124 can be used to detect SNVs and INDELs in one or more tumor samples from a single individual, with or without a matched normal sample. Assembly implies whole haplotypes and read pairs, rather than single bases, as the atomic units of biological variation and sequencing evidence, improving variant calling.
- GATK Somatic Create Mutect2 Panel of Normals 126.96.36.199 workflow creates a panel of normals (germline and artifactual sites) for use in other GATK workflows. It takes multiple normal sample callsets produced by GATK Somatic SNVs and INDELs 188.8.131.52 (Mutect2 workflow) tumor-only mode (although it is called tumor-only, normal samples are given as the input) and collates sites present in two or more samples into a sites-only VCF.
Both workflows are composed in reference to the official GATK’s WDLs.