CliqueSNV

FMLRC2 — FM-index Long Read Corrector version 2, a Rust-based hybrid error correction tool for long reads (PacBio CLR, Oxford Nanopore) using Illumina short reads as a correction guide. Builds a compr

1 shared topic • 2 shared operations

Use when running GATK Mutect2 for somatic SNV and indel detection, low allele frequency (low AF) variant calling, tumor-normal paired somatic mutation analysis, tumor-only somatic calling, panel of no

1 shared topic • 2 shared operations

Getz Lab tools (ABSOLUTE, MuTect/MuTect2) from the Broad Institute for cancer genomics. ABSOLUTE infers tumor purity, ploidy, and absolute copy numbers from segmented copy number data. MuTect2 (GATK4)

1 shared topic • 2 shared operations

medaka -- neural network-based tool from Oxford Nanopore Technologies for creating consensus sequences and calling variants from nanopore sequencing data. Polishes draft assemblies from Flye, miniasm,

1 shared topic • 2 shared operations

SvABA -- structural variant and indel caller using genome-wide local assembly. Detects deletions, insertions, duplications, inversions, and complex rearrangements from short-read (Illumina) whole-geno

1 shared topic • 2 shared operations