HaploTypo: a variant-calling pipeline for phased genomes
...ved haplotypes) reference genomes are available. However, most genetic variant calling tools do not explicit...s. HaploTypo infers the haplotype correspondence for each heterozygous variant called on a phased reference...1598 days ago
GfaViz: flexible and interactive visualization of GFA sequence graphs
...e application, it is more general, and able to represent many different types of sequence graphs, including scaffolding graphs, alignment graphs, variant graphs and splicing graphs.1563 days ago
Kevler: Reference-free variant discovery in large eukaryotic genomes
...ware for predicting de novo genetic variants without mapping reads to a r...bundance based method calls single nucleotide variants (SNVs), multinucleotide vari...on/deletion variants (indels), and structural variants (SVs) simultaneously with a...1558 days ago
FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are...1558 days ago
vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vt1558 days ago
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LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and...1537 days ago
Best Practices for Variant Calling with the GATK
...recalibration David Roazen PDF Video 03/19/15 Introduction to variant discovery: calling cohorts Louis Bergelson PDF Video 03/19/15 Variant calling and joint genotyping...1533 days ago
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