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-speci...1553 days ago
MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants
MALVA is able to genotype multi-allelic SNPs and indels without mapping reads MALVA calls correctly more indels than the most widely adopted genotyping pipelines Mappi...1553 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/vt1553 days ago
Glia: a Graph/Smith-Waterman (partial order) aligner/realigner
...local realigner. It will realign reads to a set of known (or putative) variants in a VCF, both consuming and...com/ekg/glia glia -f ~/human_g1k_v37.fasta -t 20:62900077-62902077 -v variants.vcf.gz \ -s AAATGTAAACA...1553 days ago
SeqMule: Automated human exome/genome variants detection
SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file.1532 days ago
Best Practices for Variant Calling with the GATK
...la Chandran PDF Video 03/19/15 Variant quality score recalibration Bertrand Haas PDF Video 03/19/15 Introduction to working with variants Yossi Farjoun PDF Video...1528 days ago
SvABA: Structural variation and indel detection by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-...reference with BWA-MEM and parsed to identify variants. Sequencing reads are then realigned to the contigs with BWA-MEM, and variants are scored by their read supp...1511 days ago
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GRIDSS: the Genomic Rearrangement IDentification Software Suite
...angements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided pos...1443 days ago
1431 days ago