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.pl2117 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...993 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...
3654 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...
3010 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...2687 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...3758 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...3629 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...3077 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...
2364 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...
2076 days ago
- library(vcfR) # Input the files. vcf
2061 days ago
- +15 more Bio-Scripts
Tags
- compare two BWA mapping methods with the online hg18-mapped data We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep sequencing platform <ftp://webdata:webdata@uss...
Tags: bwa, mapping, genome, vcf, align, genome
838 days ago
- Most variant calling pipelines result in files containing large quantities of variant information. The variant call format (vcf) is an increasingly popular format for this data. The format of these files and their content is discussed in the vignette ‘vcf data.’ These files ...
Tags: Bioinformatics, Analysis, NGS, vcfR, R, Visualization, VCF, Genome
2817 days ago
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Comments
- ...bsp; Customise the genotype rows printed under the VCF tracks. &nbs...
1521 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/.1545 days ago
- +3 more Comments
