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.

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.

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/>