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genetica:bioinf_process

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genetica:bioinf_process [2015/03/12 09:50]
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genetica:bioinf_process [2020/08/04 10:58]
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-There is a nice introductory [[http://seqanswers.com/wiki/How-to/exome_analysis|wiki]] to analysis of WES data, a bit outdated, but it is good to understand the basics. 
  
-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 Practives for Varaint 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_processing| Evaluation]]: callset QC, refinement and preliminary analyses 
genetica/bioinf_process.txt ยท Last modified: 2020/08/04 10:58 (external edit)