1562 days ago
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 a...1551 days ago
Best Practices for Variant Calling with the GATK
...03/19/15 Base quality score 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 Sheila...1547 days ago
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxon...porary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs ag...1461 days ago
1450 days ago
truvari: Structural variant comparison tool for VCFs
Structural variant comparison tool for VCFs Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure. Spiral Genetics Motivation1417 days ago
SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator
SVEngine (Structural Variants Engine) SVEngine is a multi-purpose and self-contained...e takes as input reference contigs in FASTA files, variant meta distribution as specified in META files (see Manual) or specific variant...1414 days ago
URMAP, an ultra-fast read mapper
...accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calling test with 30× coverage...d F-measure 0.990) with the strelka2 caller. However, GIAB reference variants are shown to be biased again...1296 days ago
1238 days ago
FiNGS: Filters for Next Generation Sequencing
Key features Filters SNVs from any variant caller to remove false positives Calculates metr...rchers with a tool to reproducibly filter somatic variants that is simple to both deplo...urable by the user. It ingests and emits standard variant...1176 days ago