NAME

       bam_pipeline - BAM pipeline of PALEOMIX suite

SYNOPSIS

       bam_pipeline [options]

DESCRIPTION

       The  PALEOMIX  pipelines  are  a  set  of  pipelines  and  tools designed to aid the rapid
       processing of High-Throughput Sequencing  (HTS)  data:  The  BAM  pipeline  processes  de-
       multiplexed  reads from one or more samples, through sequence processing and alignment, to
       generate BAM alignment files useful in  downstream  analyses;  the  Phylogenetic  pipeline
       carries  out genotyping and phylogenetic inference on BAM alignment files, either produced
       using the BAM pipeline or generated elsewhere; and the Zonkey pipeline carries out a suite
       of  analyses  on  low  coverage  equine  alignments,  in  order  to detect the presence of
       F1-hybrids in archaeological  assemblages.  In  addition,  PALEOMIX  aids  in  metagenomic
       analysis of the extracts.

       The  pipelines  have  been  designed with ancient DNA (aDNA) in mind, and includes several
       features especially useful for the analyses of ancient samples, but can  all  be  for  the
       processing of modern samples, in order to ensure consistent data processing.

       bam_pipeline is the BAM pipeline of paleomix(1).

OPTIONS

       bam_pipeline help
              Display this message

       bam_pipeline example [...]
              Create example project in folder.

       bam_pipeline makefile [...]
              Print makefile template.

       bam_pipeline dryrun [...]
              Perform dry run of pipeline on provided makefiles.  Equivalent to 'bam_pipeline run
              --dry-run [...]'.

       bam_pipeline run [...]
              Run pipeline on provided makefiles.

       bam_pipeline remap [...]
              Re-map hits from previous alignment.

SEE ALSO

       paleomix(1)

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used  for
       any other usage of the program.