1samtools-calmd(1)            Bioinformatics tools            samtools-calmd(1)
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NAME

6       samtools calmd - calculates MD and NM tags
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SYNOPSIS

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

13       Generate  the  MD  tag.  If the MD tag is already present, this command
14       will give a warning if the MD tag generated is different from  the  ex‐
15       isting tag. Output SAM by default.
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17       Calmd  can  also read and write CRAM files although in most cases it is
18       pointless as CRAM recalculates MD and NM tags on the fly.  The one  ex‐
19       ception  to  this  case  is where both input and output CRAM files have
20       been / are being created with the no_ref option.
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22       Note that some aligners do not include sequence or confidence values in
23       secondary  and  supplementary alignment records.  Where this happens in
24       SAM files, a “*” character will be seen in the SEQ  and  QUAL  columns.
25       These records will be skipped, as it is not possible to recalculate the
26       MD and NM tags without access to the query  sequence.   samtools  calmd
27       will emit a warning if any records have been skipped for this reason.
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OPTIONS

31       -A      When  used  jointly with -r this option overwrites the original
32               base quality.
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34       -e      Convert a the read base to = if it is identical to the  aligned
35               reference  base.  Indel  caller does not support the = bases at
36               the moment.
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38       -u      Output uncompressed BAM
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40       -b      Output compressed BAM
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42       -C INT  Coefficient to cap mapping quality of poorly mapped reads.  See
43               the mpileup command for details. [0]
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45       -r      Compute  the  BQ  tag  (without  -A) or cap base quality by BAQ
46               (with -A).
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48       -E      Extended BAQ calculation. This option  trades  specificity  for
49               sensitivity, though the effect is minor.
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51       --no-PG Do not add a @PG line to the header of the output file.
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53       -@, --threads INT
54               Number  of  input/output compression threads to use in addition
55               to main thread [0].
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EXAMPLES

59       o Dump BAQ applied alignment for other SNP callers:
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61           samtools calmd -bAr aln.bam > aln.baq.bam
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63         It adds and corrects the NM and MD tags at the same time.  The  calmd
64         command  also  comes  with  the  -C  option,  the  same as the one in
65         mpileup.  Apply if it helps.
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AUTHOR

69       Written by Heng Li from the Sanger Institute.
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SEE ALSO

73       samtools(1), samtools-mpileup(1)
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75       Samtools website: <http://www.htslib.org/>
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79samtools-1.15.1                  7 April 2022                samtools-calmd(1)
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