Search Results for "vcf annotation"

NGSEP is an integrated framework for analysis of short and long DNA high throughput sequencing reads. The current version provides functionalities for both de-novo and reference guided analysis of sequencing data, including genome assembly, read mapping, variants detection and genotyping and de-novo analysis of data generated from reduced representation protocols. NGSEP also provides modules for analysis of genomic variation databases (VCF files), including functional annotation, filtering...

DaMold a powerful, integrated, web-based, and user-friendly tool to filter, annotate, cross-link, and visualize NGS, Sanger, and hotspot variants. It is easy-to-use software, which provides flexible input options and accepts variants in VCF and BED formats. For each variant DaMold predicts the variant effect, such as codon change, and amino acid change. Furthermore, it cross-links each variant with more than 30 clinically relevant public databases, which contain already reported SNPs and INDELs...

... of the program and the elimination of preliminary parsing step enable to carry out the analysis at ordinary computers. VCF-Explorer presents an easy to use environment where various types of queries for the annotation and the samples can be defined. VCF-Explorer can be run at different environments and computational platforms ranging from a standard laptop to an advanced server.

This program can assemble and/or annotate genome for new genome and known genome upgrade using sequence alignment file (SAM or BAM format), sequence variant file (VCF format or five coloum table (tab-delimited, including chromosome, position, id, reference allele and alternative allele)) or new genome sequence file (FASTA format) based on reference genome sequence file (FASTA format) and annotation file (TBL, GTF, GFF, GFF3 or BED format).

This tools translates mRNA transcripts containing mutations of SNP in the VCF format. It accepts Annovar annotation files and incrorporates them into a single table containing translated SNPs. GTFplus predicts potential proteotypic peptides basing on the uniquness of the sequence.

Takes vcf file input and determines functional consequence of mutations with regard to UCSC known genes, refseq genes or ensembl genes. Will use UCSC known gene annotation by default. A correctly formatted CDS file must be used containing CDS sequences and gene table info (i.e. info from knownGene.txt for UCSC genes, refGene.txt for RefSeq or ensGene.txt for ensembl as downloaded from the UCSC downloads page [http://hgdownload.cse.ucsc.edu/downloads.html or ftp://hgdownload.cse.ucsc.edu...

... the Broad's GATK annotation functions, the VCF file and the sample's bam file.