quick_mpileup

Calculate mpileup of BED positions, without going through entire BAM file (as forced by samtools mpileup). Uses the samtools mpileup -r <region> for each entry, which is able to utilize the index of BAM files.

Requirements

To run the programs, Biopython is needed.

  a) Either install globally on machine: 
   pip install Biopython

  b) or create a virtualenv:
   virtualenv venv
   source venv/bin/activate
   pip install Biopython

Usage:

  perl fast_mpileup.pl -bam <input BAM> -o <output mpileup> -b <input bed> -f <input genome fasta>
  
   Parameters:
    -bam  input BAM file (indexed)
    -o    output mpileup file
    -f    genome fasta file
    -b    bed coordinated to perform mpileup
    
    Additional parameters:
     -e   +/- bases to extend bed coordinates (default: 0)

Mini comparison of performance

Processing BAM file (size ~2.5Gb) Number of entries: ~16,000

quick_mpileup: 6min 5sec samtools mpileup (no reference): 1min samtools mpileup (with ref):