NAME

       sambamba-mileup - make a pileup

SYNOPSIS

       sambamba  mpileup  OPTIONS  <input1.bam>  <input2.bam>  [...] [--samtools samtools mpileup
       args] [--bcftools bcftools args]

DESCRIPTION

       Parallel version of samtools mpileup in map-reduce  fashion.  Sambamba  splits  input  BAM
       files  into  chunks  and  feeds  them  to  samtools  mpileup  and, optionally, bcftools in
       parallel. The chunks are slightly overlapping  so  that  variant  calling  should  not  be
       impacted  by  these  manipulations.  The  obtained results from the multiple processes are
       combined as ordered output. Named pipes are created in TMPDIR.

       Sambamba mpileup relies on external tools and  acts  as  a  multi-core  implementation  of
       samtools + bcftools. Therefore, the following tools should be present in the PATH:

           * samtools
           * bcftools (when used)

       •   If --samtools is skipped, samtools mpileup is called with default arguments ´samtools´

       •   If  --bcftools  is  used  without parameters, samtools is called with switch ´-gu´ and
           bcftools is called as ´bcftools view -Ov´

       •   If --bcftools is skipped, bcftools is not called

OPTIONS

       •   -F, --filter=FILTER set custom filter for alignments

       •   -L, --regions=FILENAME provide BED file with regions  (no  need  to  duplicate  it  in
           samtools args); all input files must be indexed

       •   -o, --output-filename=<STDOUT> specify output filename

       •   -t, --nthreads=NTHREADS maximum number of threads to use

       •   -b, --buffer-size=4_000_000 chunk size (in bytes)

BUGS

                                           January 2015                        SAMBAMBA-MILEUP(1)