Results for "VCF"
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CrossMap: a program for convenient conversion of genome coordinates
...RCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. CrossMap is designed to l...2180 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
...ic examples of command line options and best practices for some of these technologies. NOTE: At this time HapCUT2 is for diploid organisms only. VCF input should contain diploid...2196 days ago
WhatsHap: fast and accurate read-based phasing
...al., Read-Based Phasing of Related Individuals). WhatsHap is easy to install It is easy to use: Pass in a VCF and one or more BAM files, get out a phased VCF. Supports multi-sample VCFs....2183 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
...ing them to any server. Supports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with either .tbi or .idx index), REST, and more. BAM, BigBed, BigWig, and VCF data are displayed directly f...2151 days ago
gSearch: a fast and flexible general search tool for whole-genome sequencing
gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a multi-threaded manner.2112 days ago
- VCFtools contains a Perl API (Vcf.pm) and a number of Perl scripts th...e used to perform common tasks with VCF files such as file validation...l tools support all versions of the VCF specification (3.2, 3.3, 4.0,... Perl scripts require that the VCF files are compressed by ...
2112 days ago
vcfR: a package to manipulate and visualize VCF data in R
VcfR is an R package intended to allow eas...visualization of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read...g is complete data may be written to a VCF file or converted into other...2033 days ago
jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
...erence genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simula...1759 days ago
- ...ads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants This will output a polished_variants.vcf file, that contains all...ads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants --output...
1610 days ago
- ...ta. DeepVariant relies on Nucleus, a library of Python and C++ code for reading and writing data in common genomics file formats (like SAM and VCF) designed for painless integr...
1576 days ago
