bionic (1) sambamba-pileup.1.gz

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)