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