NAME

       samtools depad - convert padded BAM to unpadded BAM

SYNOPSIS

       samtools depad [-SsCu1] [-T ref.fa] [-o output] in.bam

DESCRIPTION

       Converts  a  BAM  aligned against a padded reference to a BAM aligned against the depadded
       reference.  The padded reference may contain verbatim "*" bases in it, but "*"  bases  are
       also  counted  in  the  reference numbering.  This means that a sequence base-call aligned
       against a reference "*" is considered to be a cigar match ("M" or "X")  operator  (if  the
       base-call  is  "A", "C", "G" or "T").  After depadding the reference "*" bases are deleted
       and such aligned sequence base-calls become insertions.  Similarly  transformations  apply
       for deletions and padding cigar operations.

OPTIONS

       -S     Ignored  for compatibility with previous samtools versions.  Previously this option
              was  required  if  input  was  in  SAM  format,  but  now  the  correct  format  is
              automatically detected by examining the first few characters of input.

       -s     Output in SAM format.  The default is BAM.

       -C     Output in CRAM format.  The default is BAM.

       -u     Do not compress the output.  Applies to either BAM or CRAM output format.

       -1     Enable fastest compression level.  Only works for BAM or CRAM output.

       -T FILE
              Provides  the  padded  reference file.  Note that without this the @SQ line lengths
              will be incorrect, so for  most  use  cases  this  option  will  be  considered  as
              mandatory.

       -o FILE
              Specifies the output filename.  By default output is sent to stdout.

       --no-PG
              Do not add a @PG line to the header of the output file.

AUTHOR

       Written  by Heng Li from the Sanger Institute with extensions by Peter Cock from the James
       Hutton Institute.

SEE ALSO

       samtools(1)

       Samtools website: <http://www.htslib.org/>