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genetica:bioinf_process [2015/03/05 14:22]
vifehe created
genetica:bioinf_process [2020/08/04 10:58] (current)
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-The bioinformatic process+There is a nice introductory [[http://seqanswers.com/wiki/How-to/exome_analysis|wiki]] to analysis of WES data, a bit outdated, but it is good to understand the basics. 
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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. 
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 +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: 
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 +  * [[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:preanalyis| Preliminary analysis]]: callset QC, refinement and preliminary analyses 
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 +{{ :genetica:bioinf_process:gatk-workflow.png | GATK Best Practices Workflow}} 
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 +---- 
 +* This page displays better with Chrome than with Firefox
genetica/bioinf_process.1425565378.txt.gz · Last modified: 2020/08/04 10:48 (external edit)