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genetica:bioinf_process [2015/03/05 14:24]
vifehe
genetica:bioinf_process [2020/08/04 10:58] (current)
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 The broad institute has developed [[https://www.broadinstitute.org/gatk/|GATK]], a series of bioinformatic tools to analyze NGS data from the raw files produced by the sequencing service to the files ready for statistical analysis. The broad institute has developed [[https://www.broadinstitute.org/gatk/|GATK]], a series of bioinformatic tools to analyze NGS data from the raw files produced by the sequencing service to the files ready for statistical analysis.
  
-As GATK indicates, WES bioinformatic workflow is divided in three main sections that are meant to be performed sequentially: +As GATK indicates in his [[https://www.broadinstitute.org/gatk/guide/best-practices | Best Practices for Variant Discovery workflow]]*, WES bioinformatic workflow is divided in three main sections that are meant to be performed sequentially: 
-  * [[genetica:wes_bioinf_processing| Data cleanup]]: from raw DNAseq sequence reads (FASTQ files) to analysis-ready reads (BAM files) + 
-  * [[genetica:wes_bioinf_processing| Variant discovery]]: from reads (BAM files) to variants (VCF files) + 
-  * [[genetica:wes_bioinf_processingEvaluation]]: callset QC, refinement and preliminary analyses+  * [[genetica:bioinf_process:cleanup Sequence Data pre-process]]: from raw DNAseq sequence reads (FASTQ files) to analysis-ready reads (BAM files) 
 +  * [[genetica:bioinf_process:discovery| Variant Discovery]]: from reads (BAM files) to variants (VCF files) 
 +  * [[genetica:bioinf_process:preanalyisPreliminary analysis]]: callset QC, refinement and preliminary analyses 
 + 
 + 
 +{{ :genetica:bioinf_process:gatk-workflow.png | GATK Best Practices Workflow}} 
 + 
 + 
 +---- 
 +* This page displays better with Chrome than with Firefox
genetica/bioinf_process.1425565444.txt.gz · Last modified: 2020/08/04 10:48 (external edit)