NAME

       bamconsensus - compute rough consensus sequence from alignments

SYNOPSIS

       bamconsensus [reference=ref.fasta] < in.bam >out.fasta [options]

DESCRIPTION

       bamconsensus  reads  a  BAM,  SAM  or  CRAM  file  and computes a rough consensus based on the alignments
       contained. The input file needs to be sorted  in  coordinate  order.  The  consensus  is  written  as  an
       alignment file on the standard output channel.  The sequence names in the output file are structured as

       contig_A_B_C_D_E

       where

       A is the numeric reference id (0 based)

       B is the name of the reference sequence as given in the BAM header

       C is a numerical contig id within the contigs for a given reference id

       D is the start position on the reference sequence (inclusive)

       E is the end position on the reference sequence (exclusive)

       The  reference  key  specifying the name of a FastA reference sequence file is required. The consensus is
       constructed by computing heavy paths in local DeBruijn graphs. Consequently it is usually a patchwork  of
       the haplotypes present for diploid/polyploid genomes.

       The following key=value pairs can be given:

       reference=<ref.fasta>: reference FastA file (required)

       verbose=<1>: Valid values are

       1:     print progress report on standard error

       0:     do not print progress report

       T=<filename>: set the prefix for temporary file names

       k=<32>: k-mer size used for consensus computation (maximum 32).

       minlen=<50>: minimum length of alignments used (default 50).

       inputformat=<bam>: input format

       range=<>:  input range to be processed. This option is only valid if the input is a coordinate sorted and
       indexed BAM file

AUTHOR

       Written by German Tischler-Höhle.

REPORTING BUGS

       Report bugs to <germant@miltenyibiotec.de>

COPYRIGHT

       Copyright © 2019 German Tischler.  License GPLv3+: GNU GPL version 3 <http://gnu.org/licenses/gpl.html>
       This is free software: you are free to change and redistribute it.  There is NO WARRANTY, to  the  extent
       permitted by law.

BIOBAMBAM                                          August 2019                                   BAMCONSENSUS(1)