Variant calling Tools

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file.

Scalable gVCF merging and joint variant calling for population sequencing projects.

A high-speed next-gen sequencing structural variation caller. It calls variants based on alignment-guided positional de Bruijn graph breakpoint assembly, split read, and read pair evidence.

The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.

Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads.

LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms. It can produce nearly chromosome-scale haplotype blocks by using Nanpore ultra-long reads without the need for additional trios, chromosome conformation, and strand-seq data. LongPhase can phase a 30x human genome in ~1 minute

Strelka is an analysis package designed to detect somatic SNVs and small indels from the aligned sequencing reads of matched tumor-normal samples.

VarDict is an ultra sensitive variant caller for both single and paired sample variant calling from BAM files. VarDict implements several novel features such as amplicon bias aware variant calling from targeted sequencing experiments, rescue of long indels by realigning bwa soft clipped reads and better scalability than many Java based variant callers.

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

CIRIquant is a comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing.

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.