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

1. Methods

Read counts from BAM files generated by both pipelines were obtained using FastQC in different quality control steps performed as well as using SAMtools.
For variants comparison, VCF files were manipulated using bash scripting to:
1. Count total number of variants in whole exome and in neuropathies-related genes.
2. Obtain a list of matching genomic positions in which variants had been found by both pipelines.
Statistical metrics reports over variants were generated using VARIANT.

Sequencing coverage was evaluated in final BAM files from which variants were called in both pipelines using GATK DepthOfCoverage.
For both pipelines, sequencing coverage was assessed in exome capture kit targets only. 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 GATK DepthOfCoverage to calculate stats and build box and bar plots with ggplot2 package.