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/>

samtools-1.19.2                                  24 January 2024                               samtools-depad(1)