BOL: Results for "vcf"

Results for "vcf"

- Jit@jit.aber
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.pl
2120 days ago
- BioStar@biostar
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
+1 more Blogs

- Rahul Nayak@rahul
Bioinformatics Protocols
...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
- Jitendra Narayan@admin
CrossMap
...(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
+26 more Bookmarks

- Rahul Nayak@rahul
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
- Abhimanyu Singh@abhimanyu
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
+4 more Top-level pages

- Rahul Agarwal@raag
http://bam.iobio.io/ #bam #vcf #analysis
3448 days ago
- Jit@jit.aber
#GATK and #Picard to filter low quality variants https://insidedna.me/tutorials/view/gatk-picard-filter-vcf-variants-snp
2864 days ago
+2 more Wire posts

- ArrayGen Technologies@arraygen
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
- Strand@Strand
Joint webinar by Agilent Technologies and Strand Life Sciences on 'Analysis of Variants using GeneSpring GX' on 6 Dec
...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

- Jit@jit.aber
Downloading GATK !
...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
- Jit@jit.aber
Plot VCF with R !
library(vcfR) # Input the files. vcf
2064 days ago
+15 more Bio-Scripts

- Jit@jit.aber
Comment on "ASCIIGenome: genome browser based on command line interface and designed for running from console terminals."
...bsp; Customise the genotype rows printed under the VCF tracks. &nbs...
1524 days ago
- Jit@jit.aber
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
+3 more Comments