bam_pipeline - BAM pipeline of PALEOMIX suite

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

bam_pipeline 1.2.7                                February 2017                                  BAM_PIPELINE(1)

       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).

       bam_pipeline - BAM pipeline of PALEOMIX suite

       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.

paleomix(1)

bam_pipeline [options]