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espinos:exome_analysis [2015/08/12 10:58] cespinos [1.3 Coverage 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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| * 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]]. | * 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: | * For variants comparison, VCF files were manipulated using bash scripting to: | ||
| - | - Count total number of variants in whole exome and neuropathy-related genes. | + | - 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 founded by both pipelines. | + | - 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]]. | * Statistical metrics reports over variants were generated using [[http://wiki.opencb.org/projects/hpg/doku.php?id=variant:overview|VARIANT]]. | ||
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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. | ||
