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

6       samtools depad - convert padded BAM to unpadded BAM
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SYNOPSIS

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

13       Converts  a  BAM  aligned  against  a padded reference to a BAM aligned
14       against the depadded reference.  The padded reference may contain  ver‐
15       batim  "*" bases in it, but "*" bases are also counted in the reference
16       numbering.  This means that a sequence base-call aligned against a ref‐
17       erence  "*" is considered to be a cigar match ("M" or "X") operator (if
18       the base-call is "A", "C", "G" or "T").  After depadding the  reference
19       "*"  bases  are deleted and such aligned sequence base-calls become in‐
20       sertions.  Similarly transformations apply for  deletions  and  padding
21       cigar operations.
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OPTIONS

25       -S     Ignored for compatibility with previous samtools versions.  Pre‐
26              viously this option was required if input was in SAM format, but
27              now  the  correct  format is automatically detected by examining
28              the first few characters of input.
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30       -s     Output in SAM format.  The default is BAM.
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32       -C     Output in CRAM format.  The default is BAM.
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34       -u     Do not compress the output.  Applies to either BAM or CRAM  out‐
35              put format.
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37       -1     Enable  fastest  compression  level.  Only works for BAM or CRAM
38              output.
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40       -T FILE
41              Provides the padded reference file.  Note that without this  the
42              @SQ  line  lengths will be incorrect, so for most use cases this
43              option will be considered as mandatory.
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45       -o FILE
46              Specifies the output filename.  By default  output  is  sent  to
47              stdout.
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49       --no-PG
50              Do not add a @PG line to the header of the output file.
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AUTHOR

54       Written  by  Heng Li from the Sanger Institute with extensions by Peter
55       Cock from the James Hutton Institute.
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SEE ALSO

59       samtools(1)
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61       Samtools website: <http://www.htslib.org/>
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65samtools-1.13                     7 July 2021                samtools-depad(1)