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...1881 days ago
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...3531 days ago
3697 days ago
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...3800 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...2952 days ago
3590 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...2615 days ago
2119 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 |...1599 days ago
Comment on "Biological databases !"
all GATK bundle at ftp://ftp.broadinstitute.org/bundle/hg38/1581 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/.1587 days ago