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espinos:exome_analysis [2015/08/31 23:50] cespinos [1.2 Primary Analysis] |
espinos:exome_analysis [2016/06/24 15:51] (current) fgarcia [1.1 Pipeline's description] |
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| - | ====== Analysis of Whole-Exome Sequencing Data for the Diagnosis of Peripheral Neuropathies ====== | + | ====== Analysis of Whole-Exome Sequencing data for diagnosis of Inherited Peripheral Neuropathies ====== |
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| ==== 1.1 Pipeline's description ==== | ==== 1.1 Pipeline's description ==== | ||
| - | {{:espinos:figura_pipeline.png?680|pipeline_scheme}} | + | {{:espinos:images_ana:figura_pipeline.png?680|pipeline_scheme}} |
| ==== 1.2 Primary Analysis ==== | ==== 1.2 Primary Analysis ==== | ||
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| * 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]]. | * 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 examined neuropathies-related genes genomic coordinates with a BED file containing exome capture kit targets (SureSelect Human All Exon V5) provided by the manufacturer. | + | * 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. | * 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. | ||
