'\" t .TH samtools-calmd 1 "24 January 2024" "samtools-1.19.2" "Bioinformatics tools" .SH NAME samtools-calmd \- calculates MD and NM tags .\" .\" Copyright (C) 2008-2011, 2013-2018, 2022 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 calmd .RB [ -Eeubr ] .RB [ -C .IR capQcoef "] " aln.bam " " ref.fasta .SH DESCRIPTION .PP Generate the MD tag. If the MD tag is already present, this command will give a warning if the MD tag generated is different from the existing tag. Output SAM by default. Calmd can also read and write CRAM files although in most cases it is pointless as CRAM recalculates MD and NM tags on the fly. The one exception to this case is where both input and output CRAM files have been / are being created with the \fIno_ref\fR option. Note that some aligners do not include sequence or confidence values in secondary and supplementary alignment records. Where this happens in SAM files, a \(lq*\(rq character will be seen in the \fBSEQ\fR and \fBQUAL\fR columns. These records will be skipped, as it is not possible to recalculate the MD and NM tags without access to the query sequence. .B samtools calmd will emit a warning if any records have been skipped for this reason. Calmd works best on position-sorted input files, as with these it can stream through the reference sequence and so doesn't have to store much reference data at any one time. For other orderings, it may have to switch to a caching mode which keeps the reference sequences in memory. This will result in calmd using more memory (up to the full size of the reference) than it would in the position-sorted case. Note also that versions of samtools calmd up to 1.16.1 should only be used on position sorted inputs as they could be very slow when run on other orderings. .SH OPTIONS .TP 8 .B -A When used jointly with .B -r this option overwrites the original base quality. .TP 8 .B -e Convert a the read base to = if it is identical to the aligned reference base. Indel caller does not support the = bases at the moment. .TP .B -u Output uncompressed BAM .TP .B -b Output compressed BAM .TP .BI -C \ INT Coefficient to cap mapping quality of poorly mapped reads. See the .B mpileup command for details. [0] .TP .B -r Compute the BQ tag (without -A) or cap base quality by BAQ (with -A). .TP .B -E Extended BAQ calculation. This option trades specificity for sensitivity, though the effect is minor. .TP .BI --no-PG Do not add a @PG line to the header of the output file. .TP .BI "-@, --threads " INT Number of input/output compression threads to use in addition to main thread [0]. .SH EXAMPLES .IP o 2 Dump BAQ applied alignment for other SNP callers: .EX 2 samtools calmd -bAr aln.bam > aln.baq.bam .EE It adds and corrects the .B NM and .B MD tags at the same time. The .B calmd command also comes with the .B -C option, the same as the one in .BR mpileup . Apply if it helps. .SH AUTHOR .PP Written by Heng Li from the Sanger Institute. .SH SEE ALSO .IR samtools (1), .IR samtools-mpileup (1) .PP Samtools website: