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.