/bamMetrics

Tool to generate bam statistics and pdf/html reports.

Primary LanguagePerlMIT LicenseMIT

bamMetrics

Tool to generate bam statistics and pdf/html reports. To be used on the UMC hpc cluster.

Usage

perl bamMetrics.pl [options] -bam <bamfile1.bam> -bam <bamfile2.bam>

Required:

  • bam

Optional (some have default settings):

Whole genome sequencing statistics

  • wgs
  • coverage_cap 250

RNA sequencing statistics

  • rna
  • ref_flat refFlat.gz
  • strand [NONE, FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND]
  • ribosomal_intervals rRNA.intervallist

Capture sequencing statistics (exome)

  • capture
  • targets targets.bed
  • baits baits.bed

Other

  • output_dir ./bamMetrics
  • run_name bamMetrics
  • genome genome.fasta
  • queue all.q
  • queue_time 2:0:0
  • queue_threads 1
  • queue_mem 8
  • picard_path /path/to/picard/

Dependencies

  • Perl
  • R
  • sge
  • Picard >= 1.119
  • Sambamba

Perl Modules

  • strict
  • Getopt::Long
  • Pod::Usage
  • POSIX
  • Cwd
  • File::Basename

R packages

  • ggplot2
  • knitr
  • markdown
  • reshape
  • xtable
  • tools
  • brew
  • GetoptLong