1samtools-calmd(1) Bioinformatics tools samtools-calmd(1)
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6 samtools calmd - calculates MD and NM tags
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9 samtools calmd [-Eeubr] [-C capQcoef] aln.bam ref.fasta
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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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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
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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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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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69 Written by Heng Li from the Sanger Institute.
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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)