'\" t .TH samtools-depad 1 "24 January 2024" "samtools-1.19.2" "Bioinformatics tools" .SH NAME samtools-depad \- convert padded BAM to unpadded BAM .\" .\" Copyright (C) 2008-2011, 2013-2018 Genome Research Ltd. .\" Portions copyright (C) 2010, 2011 Broad Institute. .\" .\" Author: Heng Li .\" Author: Joshua C. Randall .\" .\" Permission is hereby granted, free of charge, to any person obtaining a .\" copy of this software and associated documentation files (the "Software"), .\" to deal in the Software without restriction, including without limitation .\" the rights to use, copy, modify, merge, publish, distribute, sublicense, .\" and/or sell copies of the Software, and to permit persons to whom the .\" Software is furnished to do so, subject to the following conditions: .\" .\" The above copyright notice and this permission notice shall be included in .\" all copies or substantial portions of the Software. .\" .\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR .\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, .\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL .\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER .\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING .\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER .\" DEALINGS IN THE SOFTWARE. . .\" For code blocks and examples (cf groff's Ultrix-specific man macros) .de EX . in +\\$1 . nf . ft CR .. .de EE . ft . fi . in .. . .SH SYNOPSIS .PP samtools depad .RB [ -SsCu1 ] .RB [ -T .IR ref.fa ] .RB [ -o .IR output "] " in.bam .SH DESCRIPTION .PP 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. .SH OPTIONS .TP .B -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. .TP .B -s Output in SAM format. The default is BAM. .TP .B -C Output in CRAM format. The default is BAM. .TP .B -u Do not compress the output. Applies to either BAM or CRAM output format. .TP .B -1 Enable fastest compression level. Only works for BAM or CRAM output. .TP .BI "-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. .TP .BI "-o " FILE Specifies the output filename. By default output is sent to stdout. .TP .BI --no-PG Do not add a @PG line to the header of the output file. .SH AUTHOR .PP Written by Heng Li from the Sanger Institute with extensions by Peter Cock from the James Hutton Institute. .SH SEE ALSO .IR samtools (1) .PP Samtools website: