BAM Pipeline

Table of Contents:

• Overview of analytical steps
• Software requirements
  • Testing the pipeline
• Configuring the BAM pipeline
• Pipeline usage
  • Creating a makefile
    • Default options
  • Reference genomes (prefixes)
  • Specifying read data
  • The final makefile
• Makefile description
  • Specifying command-line options
  • Options
    • General Options
    • Adapter Trimming
    • Short read aligners
      • Short read aligners - BWA
      • Short read aligners - Bowtie2
    • mapDamage options
    • Excluding read-types
    • Optional features
  • Prefixes
    • Regions of interest
    • Adding multiple prefixes
  • Targets
    • Including already trimmed reads
    • Overriding global settings
• File structure
  • Primary results
  • Intermediate results
    • Processed reads
    • Mapped reads

The BAM Pipeline is a pipeline designed for the processing of demultiplexed high-throughput sequencing (HTS) data, primarily that generated from Illumina high-throughput sequencing platforms.

The pipeline carries out trimming of adapter sequences, filtering of low quality reads, merging of overlapping mate-pairs to reduce the error rate, mapping of reads using against one or more reference genomes / sequences, filtering of PCR duplicates, analyses and correction of post-mortem DNA damage, estimation of coverage, depth-of-coverage histograms, and more. To ensure the correctness of the results, the pipeline invokes frequent validation of intermediate results and attempts to detect common errors in input files.

To allow tailoring of the process to the needs of individual projects, many features may be disabled, and the behavior of most programs can be tweaked to suit the specific of a given project.