Results for "vcf"
Blogs
Converting a VCF into a FASTA given some reference !
...(Heng Li) provides a Perl script vcfutils.pl which does this, the function vcf2fq (lines 469-528) This...e.g. this by David Eccles ./vcf2fq.pl -f <input.fasta>....com/lh3/samtools/blob/master/bcftools/vcfutils.pl2120 days ago
Bioinformatics tools for telomere to telomere assembly !
...riants (Yuanyuan Cheng @Yuanyuan929)● svpack – tools for filtering, comparing, and annotating structural variant (SV) calls in VCF format (Aaron Wenger)● J...996 days ago
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Bookmarks
- ...up* GATK: Unified Genotyper* FreeBayesEach of these tools takes as its input a BAM file of aligned reads and generates a list of likely variants in VCF format Pipelines are for tho...
3657 days ago
- ...(GRCh37), 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 lif...
3013 days ago
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Pages
Genome Assembly Tools and Software - PART2 !!
...es can currently be used to create accurate pairwise SNP phasings.Given a set of aligned sequence reads in a SAM file and a set of variant calls in VCF format, HAPCOMPASS will assem...2690 days ago
Top-level pages
List of bioinformatics open source projects/software.
...analysis of functional genomics experiments, e.g. RNA-seq or ChIP-seq. GeneTalk http://www.gene-talk.de/ Tool for filtering sequence variants in VCF files. Network for scientists...3761 days ago
Perl one-liner for bioinformatician !!!
...enomics text. There are several "standardized" file formats (FASTQ, SAM, VCF, etc.) and some tools for manipulating them (fastx toolkit, samtools, vcftools, etc.), there are still...3632 days ago
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Wire posts
News
ArrayGen Next Generation Genome Browser Coming Soon !!!
...s. It is platform independent and much simpler to use. The main features are, it supports many standard file formats such as GFF, BED, GTF, FASTA, VCF, BAM and it can be integrated...3080 days ago
- ...pository for identification of germline and somatic mutations. This is a simple workflow for selection of homozygous SNPs from Variant Call Format (VCF) file and for filtering based...
2367 days ago
Bio-Scripts
- ...ocessGermlineCNVCalls Create a VCF given the output of GermlineC...fingerprint from the supplied input (SAM/BAM or VCF) file and compares it to the...Creates an index for a feature file, e.g. VCF or BED file. ParallelCop...
2079 days ago
- library(vcfR) # Input the files. vcf
2064 days ago
- +15 more Bio-Scripts
Tags
- Genome Browser is the platform/database used for searching and retreiving sequences and annotation of genomes belong to various eukaryotes, prokaryotes, etc. Following are the weblink for different available browsers: http://www.ensembl.org/index.html http://ensemblgenomes.org/ http://genome....
Tags: Genome Browser, Organism, Plant, Animal, Bacteria, fungi, Genome Sequence, DNA, Sequencing, Annotation, SNP, gff, gtf, gff3, vcf, bed
3919 days ago
Convert VCF to tab-deilimited table
Performed with GATK : java -Xmx8g -jar GenomeAnalysisTK.jar \ -T VariantsToTable \ -R reference.fa \ -V reference_genomes_GT.vcf \ -F CHROM -F POS -F REF -F ALT -GF GT \ -o reference_genomes_GT.table multiple_sample.vcf should also be converted to multiple_sample_GT.table using this...Tags: Convert, VCF, tab-deilimited, table
2186 days ago
Comments
- ...bsp; Customise the genotype rows printed under the VCF tracks. &nbs...
1524 days ago
Comment on "Biological databases !"
NCBI released a set of GATK-specific dbSNP VCF's, with the "chr" attached. Those can be accessed at ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/.1547 days ago
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