CIGAR strings and 'N' symbols

[pieffe]

Just wondering if anybody can help me to understand the following example:


ref: AC GTACGT
r1 : ACCGTACGT
r2 : AC......T

Will the CIGARs be:

2M1I6M
2M6N1M

OR will it be:
2M1I6M
2M5N1M



In other words, if there are alignment positions with possible insertions in the reference, will the skipped positions (Ns) take into account these possible insertions?


Also, how do mappers determine segments with skipped N positions?

Thanks!

[nilshomer]

Just wondering if anybody can help me to understand the following example:


ref: AC GTACGT
r1 : ACCGTACGT
r2 : AC......T

Will the CIGARs be:

2M1I6M
2M6N1M

OR will it be:
2M1I6M
2M5N1M



In other words, if there are alignment positions with possible insertions in the reference, will the skipped positions (Ns) take into account these possible insertions?


Also, how do mappers determine segments with skipped N positions?

Thanks!

ref: AC GTACGT
r1 :  ACCGTACGT
r2 :  AC......T

In my opinion r2 is not valid. The "." is meant to represent skipping a base within the read that correspond to a reference base, not an insertion. The inserted base should be represented with an "N" if it the inserted base is unknown. Therefore r2 should be "ACN.....T" and the cigar would be 2M1I5N1M.

You may want to send an email to the samtools-help mailing list for clarification.

[pieffe]

Thank you for your prompt reply. I think what you says makes sense. However, in the SAM specifications, there is an example where the alignment is spliced and the read does not have a 'N' symbol at all, and yet the cigar has 32N in it.

I tried to use samtools to dig into this, but got even more confused. I guess I am going to ask to the authors of samtools for clarifications. I will post what I find out.

Thanks again!

[nilshomer]

Thank you for your prompt reply. I think what you says makes sense. However, in the SAM specifications, there is an example where the alignment is spliced and the read does not have a 'N' symbol at all, and yet the cigar has 32N in it.

I tried to use samtools to dig into this, but got even more confused. I guess I am going to ask to the authors of samtools for clarifications. I will post what I find out.

Thanks again!

The "N" symbol in the read indicates a missing base, the "N" symbol in the cigar indicates a skipped reference base. The splice alignment has no "N" bases but skips reference bases, hence the "N" in the cigar string.

[pieffe]

Hi Nils,

I think I was too quick to email you a reply. I re-read your answer and you probably are right. The example in the SAM paper won't need N symbols in the read, since there are no insertions in reference.
I guess that, if I am not misunderstanding, whenever a read has a I symbol in the cigar, other reads will either have P symbols in the cigar or they will have a N symbol in the read and a I symbol in the cigar.

Thanks again,
PF