Deciphering cigar strings

Question

[phosphorus]

Hi everyone,

I'm trying to analyse a bam file but when I viewed it on samtools I noticed its cigar strings are all composed of unfamiliar characters.

Here is an example:

AAAGGGGGGTTGCCTGCCCTGTCTCCTACCTGAGGCTGAGGAAGGAGAAGGGGATGCACTGTTGGGGAGGCAGCTGTAACTCAAAGCCGTAGCCTCTGTTCCCACGAAGGCAGGGCCATCCGGCACCAAAGCGATTCTGCCAGCATAGTG     A7AA7(7</7AKKKAFFFKK<<<KKKKKKKK7AAFK/A(</FFKKKK//<7FK/A<<<AFA<<FKKA<<(AFAKKAF(FFAKA/7AK<(/7/AF/F<A<FKK7FKK//<<FFKFKK7</A(AA7(AK7FFA(A/<AA/AKF7<A/(7(AF

Another example:

TACCTGAGGCTGAGGAAGGAGAAGGGGATGCACTGTTGGGGAGGCAGCTGTAACTCAAAGCCTTAGCCTCTGTTCCCACGAAGGCAGGGCCATCAGGCACCAAAGGGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGC      AFFKKKK<FK<KKKKKKKKKKFKKKKKK7<KKKFKKK<KKKKFFKKKKKKKKKKFKKKKKKKAKKFKK/AAKK<AFKKKFAKA<KKKKKKKF<K<7<<FKK<FFAFK7/FFA<AFAKKFK<AKFFKAK77A<FFKK7AKF7AKAFFA<A

What do A, F, J, K, <, 7, /, ( mean? Is there a command/tool I can use to translate them into more familiar cigar string characters?

[Pierre Lindenbaum]

this is not the cigar string.

Answer 1

[swbarnes2]

Those look like quality strings, not CIGAR strings.

Answer 2

[Jeremy]

Those might be the quality scores. The CIGAR string should be in Column 6 of a SAM file. See the SAM/BAM Format Specification:

SAM/BAM Format