Results for "gatk"
Blogs
Understanding reads mapping and flags !
...not have large overlaps, it called representative alighment, for other alignment positions, we called them supplementary alignment. It seems that GATK can realignment those represe...1830 days ago
Bookmarks
Next Generation Sequencing (NGS) Tutorials
...ation sequencing data. http://www.ncbi.nlm.nih.gov/pubmed/23657089 GATK: a Toolkit for Genome Analysis http://www.broadinstitute.org/gatk/ Metagenomics:http://www.nbi...3481 days ago
- ...f three statistically-based variant detection tools:* SAMtools: Mpileup* GATK: Unified Genotyper* FreeBayes...ften allow more control over branching and iteration logic. WGS/exome GATK-based variant calling pipelin...
3646 days ago
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Top-level pages
List of bioinformatics open source projects/software.
...ulograms, Substitution models) UGENE integrated bioinformatics tools Visomics bioinformatics tools for omics data Genome Analysis Toolkit 1.0 (GATK 1.0) a software package to a...3750 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...: requires BAM files (aligned with GATK) Reference Genome: indexed F...ade a reference is needed for both GATK and BWA and a SNP (dbSNP!) da...SNV-PPILP Description: Refines GATK’s Unified Genotyper SNV...on. Input: Maq, gff, CASAVA, VCF, GATK bed, custom Output: “d...2902 days ago
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Wire posts
News
- ...next generation sequencing data sets. Scalpel, which is open source and available for download on SourceForge, outperformed the popular tools GATK HaplotypeCaller and SOAPindel...
3540 days ago
Webinar on Fast and Accurate DNA Variant Calling on 26 Apr 2017
...nd NGS v3.0 best-practices: a workflow that identifies highly accurate variants from raw reads. Our best practices workflow is twice as fast as its GATK counterpart, and results in p...2564 days ago
Bio-Scripts
- ...s://github.com/broadinstitute/gatk/releases/download/4.0.2.1/gatk-4.0.2.1.zip --2018-08-30 11:...endra@jitendra-UNLOCK-INSTALL[gatk-4.0.2.1] ./gatk --list...Compare GATK's internal pileup to a refere...e reads. MarkDuplicatesGATK (EX...
2068 days ago
Bash command to install GATK, Bedtools and SnpEff !
(my_GATK) [wsu29@bladeamd-2 tmp]$ conda install gatk Collecting package metadata...py38_0 156 KB gatk-3.8 |...:certifi-2019.11.28-py38_0 gatk bioconda/noarch...#################### | 100% gatk-3.8 | 8 KB |...1548 days ago
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Tags
Best Practices for Variant Calling with the GATK
The presentations below were filmed during the March 2015 GATK Workshop, part of the BroadE Workshop series. At the time of this workshop, the current version of Broad’s Genome Analysis Toolkit (GATK) was version 3.3. Genome Analysis Toolkit 0...Tags: Best, Practices, Variant, Calling, GATK
1527 days ago
Comments
Comment on "Biological databases !"
all GATK bundle at ftp://ftp.broadinstitute.org/bundle/hg38/1531 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/.1537 days ago
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