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samtools-depad(1)	     Bioinformatics tools	     samtools-depad(1)

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  ver-
       batim  "*" bases	in it, but "*" bases are also counted in the reference
       numbering.  This	means that a sequence base-call	aligned	against	a ref-
       erence  "*" 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 in-
       sertions.  Similarly transformations apply for  deletions  and  padding
       cigar operations.

OPTIONS
       -S     Ignored for compatibility	with previous samtools versions.  Pre-
	      viously 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  out-
	      put 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-1.12			 17 March 2021		     samtools-depad(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO

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