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.

-@, --threads INT

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

EXAMPLES

• 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/>