Results for "vcf"

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  • Genome Browsers

    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

    3877 days ago

  • http://bam.iobio.io/ #bam #vcf #analysis

    Tags: bam, vcf, analysis

    3406 days ago

  • https://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it #VCF #vcf #SNP

    Tags: VCF, vcf, SNP

    2078 days ago

  • Building a #consensus sequence with #vcf files https://cbc.brown.edu/blog/consensus-vcf/

    Tags: consensus, vcf

    1485 days ago

  • VCF Compare !

    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

    799 days ago

  • vcfR

    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

    2778 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

    2144 days ago

  • Converting a VCF into a FASTA given some reference !

    Samtools/BCFtools (Heng Li) provides a Perl script vcfutils.pl which does this, the function vcf2fq (lines 469-528) This script has been modified by others to convert InDels as well, e.g. this by David Eccles ./vcf2fq.pl -f <input.fasta> <all-site.vcf> ...

    Tags: Convert, VCF, FASTA, reference, genome, assembly, phase

    2078 days ago

  • VCFtools: perform common tasks with VCF files such as file validation, file merging, intersecting, complements

    VCFtools contains a Perl API (Vcf.pm) and a number of Perl scripts that can be used to perform common tasks with VCF files such as file validation, file merging, intersecting, complements, etc. The Perl tools support all versions of the VCF specification (3.2, 3.3, 4.0, 4.1 and 4.2), nevertheless...

    Tags: VCFtools, Perl, API, Vcf.pm, Perl, scripts, VCF, validation, file, merging, intersecting, complements

    2060 days ago