samtools calmd description
Samtools calmd generates 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. The MD field aims to achieve SNP or indel calling without looking at the reference. For example, a string *10A5^AC6* means from the leftmost reference base in the alignment, there are 10 matches followed by an A on the reference which is different from the aligned read base; the next 5 reference bases are matches followed by a 2bp deletion from the reference; the deleted sequence is AC; the last 6 bases are matches. The MD field ought to match the CIGAR string
Parent program: samtools
SAMTools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. It is very convinient for handling reads mapped to reference genome. Normally SAMtools is used in intermediate step between raw read mapping and SNP or variants callingm, because it allows to effeciently store mapped reads.