====== Analysis of Whole-Exome Sequencing data for diagnosis of Inherited Peripheral Neuropathies ======




===== 1. Methods =====


==== 1.1 Pipeline's description ====

{{:espinos:images_ana:figura_pipeline.png?680|pipeline_scheme}}

==== 1.2 Primary Analysis ====
 
  * Read counts from BAM files generated by both pipelines were obtained using [[http://www.bioinformatics.babraham.ac.uk/projects/fastqc/|FastQC]] in different quality control steps performed as well as using [[http://www.htslib.org/|SAMtools]].
  * For variants comparison, VCF files were manipulated using bash scripting to:
    - Count total number of variants in whole exome and in neuropathies-related genes. 
    - Obtain a list of matching genomic positions in which variants had been found by both pipelines.
  * Statistical metrics reports over variants were generated using [[http://wiki.opencb.org/projects/hpg/doku.php?id=variant:overview|VARIANT]].


==== 1.3 Coverage Analysis ====

  * Sequencing coverage was evaluated in final BAM files from which variants were called in both pipelines using [[https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_coverage_DepthOfCoverage.php|GATK DepthOfCoverage]]. 
  * For both pipelines, sequencing coverage was assessed in exome capture kit targets only. [[http://bedtools.readthedocs.org/en/latest/|BEDtools]] was used to intersect a list of significant neuropathies-related genes genomic coordinates with a BED file containing exome capture kit targets (SureSelect Human All Exon V5) provided by the manufacturer.
  * R scripts were used to manipulate coverage data generated by [[https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_coverage_DepthOfCoverage.php|GATK DepthOfCoverage]] to calculate stats and build box and bar plots with [[http://docs.ggplot2.org/current/|ggplot2]] package.

===== 2. Results =====

==== 2.1 Primary Analysis ==== 

  * **[[Results.Primary.Analysis|Sequence processing]]**
  * **[[Results.Primary.Analysis.2|Variants comparison]]**

==== 2.2 Coverage Analysis ==== 

  * **[[Results.Coverage.Analysis|All exome coverage]]**
  * **[[Results.Coverage.Analysis.2|Neuropathies-related genes coverage]]**