Ubuntu Manpage: samtools-calmd - calculates MD and NM tags

NAME

       samtools-calmd - calculates MD and NM tags

SYNOPSIS

       samtools calmd [-Eeubr] [-C capQcoef] aln.bam ref.fasta

DESCRIPTION

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 no_ref 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 “*” character will be
seen in the SEQ and QUAL columns. These records will be skipped, as it is not possible to
recalculate the MD and NM tags without access to the query sequence. 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.

OPTIONS

       -A      When used jointly with -r this option overwrites the original base quality.

       -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.

       -u      Output uncompressed BAM

       -b      Output compressed BAM

       -C INT  Coefficient to cap mapping quality of poorly mapped reads. See the mpileup command
               for details. [0]

       -r      Compute the BQ tag (without -A) or cap base quality by BAQ (with -A).

       -E      Extended BAQ calculation. This option trades specificity for  sensitivity,  though
               the effect is minor.

       --no-PG Do not add a @PG line to the header of the output file.

       -@, --threads INT
               Number of input/output compression threads to use in addition to main thread [0].

EXAMPLES

       o Dump BAQ applied alignment for other SNP callers:

           samtools calmd -bAr aln.bam > aln.baq.bam

         It  adds  and corrects the NM and MD tags at the same time. The calmd command also comes
         with the -C option, the same as the one in mpileup.  Apply if it helps.

AUTHOR