A Java-based DNA variant calling tool for Next-Generation Sequencing alignment data. SolSNP uses a modified Kolmogorov-Smirnov statistic and data filtering to confidently and quickly call variants on high-coverage aligned genomes.
Does anyone have any guidance or suggestions for variant calling RADseq and WGS datasets to generate a single population genomic dataset? Both datasets represent population-level …
I have 63 DNA-seq files which I put through the GATK variant calling pipeline (https://gencore.bio.nyu.edu/variant-calling-pipeline-gatk4/) This is my first time doing this and I am …
Hi, I'm working with dna-seq data from pancreatic cancer patients, and is trying to create an ensemble of somatic variant calls from different variant callers. …
I am performing alignment to reference and variant calling for same sample using freebayes. Both the technical replicates were sequenced on MiSeq PE 250. The …
My understanding is that Haplotypecaller is specifically designed to call variant from DNA-Seq data. However, RNA-Seq has different (more complicated) allele frequency than DNA-Seq. So …
From the [LoFreq Wiki][1]: [LoFreq][2] is a fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data. It is designed to robustly …
Using the Bioconductor [VariantAnnotation][1] Package to [Annotate Genetic Variants][2] > The VariantAnnotation package has facilities for reading in all or portions of Variant Call Format …
[SVA][1]: [software for annotating and visualizing sequenced human genomes][2] > Sequence Variant Analyzer (SVA), a software tool that assigns a predicted biological function to variants …
[Variant Annotation Tool][1] [A computational framework to functionally annotate variants in personal genomes using a cloud-computing environment][2] > The functional annotation of variants obtained through …
[VarioWatch][1]: [providing large-scale and comprehensive annotations on human genomic variants in the next generation sequencing era][2]. A web based tool for visualization and annotation of …