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 Motivation1403 days ago
SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator
SVEngine (Structural Variants Engine) SVEngine is a multi-purpose and sel...akes as input reference contigs in FASTA files, variant meta distribution as specified in META files (see Manual) or specific variant information as specified in V...1400 days ago
URMAP, an ultra-fast read mapper
...e accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calling test with 30× c...and F-measure 0.990) with the strelka2 caller. However, GIAB reference variants are shown to be biased again...1282 days ago
1224 days ago
FiNGS: Filters for Next Generation Sequencing
Key features Filters SNVs from any variant caller to remove false positives Cal...rs with a tool to reproducibly filter somatic variants that is simple to both deplo...le by the user. It ingests and emits standard variant call format (VCF) files and w...1162 days ago
QuasiModo - Quasispecies Metric Determination on Omics
...V benchmarking study. In this study we evaluated genome assemblers and variant callers on 10 in vitro genera...bundance ratios. This tool can also be used to evaluate assemblies and variant calling results on other simi...1042 days ago
Calling variants in non-diploid systems
The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between t...equencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts...1042 days ago
869 days ago
Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
Merfin, a k-mer based variant-filtering algorithm for improved accuracy in g...nome assembly polishing. Merfin evaluates each variant based on the expected k-...ently of the quality of the read alignment and variant caller’s internal score...761 days ago
Minda: a tool for evaluating structural variant (SV) callers
Minda is a tool for evaluating structural variant (SV) callers that standardizes VCF records for compatibility with both germline and somatic SV callers, benchmarks against a single VCF input file, or benchmarks against an ensemble call set created from multiple VCF input files.34 days ago