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.

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

       Written by Heng Li from the Sanger Institute.

SEE ALSO

       samtools(1), samtools-mpileup(1)

       Samtools website: <http://www.htslib.org/>