Cigar-op

[tindinh]

Hi everyone, I am little confused Cigar and cigar-op. Can you explain the diff? Thank you!

[lindenb]

a cigar string is an array of cigar elements
a cigar element is a pair of cigar-operator, cigar-length
cigar-operator (H,S,E,X,=,I,D...) define the type of pairwise alignment (e.g D=deletion from REF)
cigar-length is the length of the operation (e;g: D100 deletion of 100bp)

[tindinh]

a cigar string is an array of cigar elements
a cigar element is a pair of cigar-operator, cigar-length
cigar-operator (H,S,E,X,=,I,D...) define the type of pairwise alignment (e.g D=deletion from REF)
cigar-length is the length of the operation (e;g: D100 deletion of 100bp)

Can you give me the meaning of all those signals H,S,E,X,=, I,D,.. or which material I can look up them?

[Brian Bushnell]

Here's the specification:

http://samtools.github.io/hts-specs/SAMv1.pdf