SAMtools - * character in pileup file

[JosieR]

Hi all,

I'm trying to interpret some SAMtools pileup data I generated, and I ran into a character that isn't explained in the pileup format explanation page: http://samtools.sourceforge.net/pileup.shtml
Here's what my data look like:

X 24364 T 34 ,..,.,.,,...,,.,.,,,,,,,.,,,,,.*..
X 24365 C 36 ,$T$.,.,.,,...,,.,.,,,,,,,.,,,,,.*..^F.^:.
X 24366 A 34 .,.-1T,.c,...,,.,.,,,,,,,.,,,,,.,....
X 24367 T 36 .,*,.,,...,,.,.,,,,,,,.,,,,,.,....^:a^F,
X 24368 T 36 .$,.,.,,...,,.,.,,,,,,,.,,,,,.,....gg
X 24369 T 36 ,$._,.,,...,,.,.,,,,,,,.,,,,,.,....ag^F.

So you'll see that lines 24364, 24365, and 24367 contain positions annotated by "*". What does this mean? The pileup format explanation page is clear about all the other characters just not this one...

[sdriscoll]

I wonder if those are the same notation as you see in their sample images of the viewer on http://samtools.sourceforge.net/tview.shtml

I'm not sure what those mean either. I was going to guess that they note insertions or deletions but it seems they have a separate notation for that. Did you generate this pileup data using SAMtools?

[JosieR]

I wonder if those are the same notation as you see in their sample images of the viewer on http://samtools.sourceforge.net/tview.shtml

I'm not sure what those mean either. I was going to guess that they note insertions or deletions but it seems they have a separate notation for that. Did you generate this pileup data using SAMtools?

Yep, I used SAMtools to create this pileup data and the original alignment was done using BWA (I think bwa's first author is the same as SAMtools'?). I will probably try emailing the author directly if no one replies soon.

[nilshomer]

They are placeholders for deletions so that the coverage column matches the number of characters (answered in other posts; please search them first).

[JosieR]

I don't think this answer works for my case. These characters are appearing at positions that don't have annotated insertions or deletions e.g.:
X 24466 G 33 ,,,...,,.,,..,,,,,,...,,.,,,,.*.. fefbea`fffdBedfff_affffdWcbbbfbfY

According to the http://samtools.sourceforge.net/pileup.shtml pileup faq page, an insertion or deletion should be annotated e.g. -1 or +1 etc:
X 24573 T 31 .G,C.,....,,,,,,.,,,g,,,,,.*,,,+1c dBfBafaac`feedd_cedfBdB_BdXBcB`

Why would there have to be a placeholder in the first case when there is no insertion or deletion in the pileup?

Also, I did search first and found nothing related to "*". pileup, and SAMtools - but thank you for taking the time to answer. Perhaps if you direct me to those threads I could find further clarification there.

[nilshomer]

I don't think this answer works for my case. These characters are appearing at positions that don't have annotated insertions or deletions e.g.:
X 24466 G 33 ,,,...,,.,,..,,,,,,...,,.,,,,.*.. fefbea`fffdBedfff_affffdWcbbbfbfY

According to the http://samtools.sourceforge.net/pileup.shtml pileup faq page, an insertion or deletion should be annotated e.g. -1 or +1 etc:
X 24573 T 31 .G,C.,....,,,,,,.,,,g,,,,,.*,,,+1c dBfBafaac`feedd_cedfBdB_BdXBcB`

Why would there have to be a placeholder in the first case when there is no insertion or deletion in the pileup?

Also, I did search first and found nothing related to "*". pileup, and SAMtools - but thank you for taking the time to answer. Perhaps if you direct me to those threads I could find further clarification there.

See the SAMtools FAQ's answer: http://sourceforge.net/apps/mediawik...at_are_they.3F

[JosieR]

See the SAMtools FAQ's answer: http://sourceforge.net/apps/mediawik...at_are_they.3F

Ok, but what's the difference between a deletion that is annotated * versus one that is annotated -1A ?

[lh3]

Same......

[JosieR]

Same......

But is there a reason why the program will sometimes put -1A and sometimes put *?

[foxyg]

NM, figured it out