Samtools - pileup format question

[Hena]

Hi,

I'm using pileup to make indel and snp calls. But I noticed a strangeness that isn't marked in the help page. There is a '*' in the read bases column (9th). What does that mean?


bacterial_genome 24721 G S 151 151 55 354 .$,$.,..,,,..,,....,.,.,,,,..C,..,,,,.,,,.,,,,,,,,.*,..cc,c..,,..,,,c...,,,,.,.,,,,,ccc,,.,,cccc,,.,,..,c,,.,,t,c..cccc,cc,,c..,,,,cc,c,,c,,...,,cccc,c,,,c,ccc,,c,,,,.....cc,c,,...c,.,,,,,,....,cccc,.cc,,.....,.c,,.....,,ccccc,,..,,c,c...,c,c,c,,c...,c*.......ccc.cccccc.cc,c,.c.c,,.,...,ccc,ccccccc.ccc.c,,,.ccc.,,c,cc,c,.cc,cc.cc,,c,.c,c,cc..,cc,c,,,c,^].^], aaXUB^^baaaba`a_a_PYaab_a`aE_\BYXa^aaa[]aaaX_aabaDaSRGMTI`a^W``\YFHabbUBOT_M^TPTIFBDDQ]^OFBSQBLDa[Sa]LRML`FUBBRVaOHBBBQQYLGaYURFFBBHGHYFWMbbbDODBBBDBLHHFBBBBLFaOGbJa`[aaBHNHHZaPPEBa]BHDDB_`Z^BBBLPFaXPLO]Za_aF`BGE__baaLFNDQBNLJaaGSBFF^YaHMHBGFEBBaUbFBIb[b_ba]BEBbFBBBBE`BBFBLbBbBBBbL`__BBYBGOBBBBHFbMOFbBQBBa^RBbJLBBBBBEGaBBRHMbEBEGEFbLGBBBHaaHWBLBJFTVBaQ

[wumblehoots]

Hi Hena,

I'd love to help, but can't. I have exactly the same problem though, so if anyone can explain the presence of the asterisk I'd love to know.

In my case I have the pileup output line:
1 973543 G 8 .,.*...c 02=>?C,) ~bmomtm~

generated using the command:
samtools pileup -s -l coords.txt ftp://ftp.1000genomes.ebi.ac.uk/vol1...32.2009_07.bam -f reference/human_b36_female.fa

The asterisk is not documented on the help page here:

http://samtools.sourceforge.net/pileup.shtml

Cheers

[lh3]

Start stands for a deletion. It is a place holder.

[Hena]

Why is there two ways of marking deletions? As the page mentions that this '-[0-9]+[ACGTNacgtn]+' is a pattern for deletion. Also it seems that the * has a quality score in base quality column.

I can understand * in column 3 marks for deletion and insertion row, but it seems odd in the read bases column.

[wumblehoots]

I think the implication is that the deletion information (i.e. how much has been deleted and what) would be in a previous alignment column, and the asterisk appears in the appropriate number of subsequent columns as a placeholder for that sequence?

I'm not sure why it has a quality score associated with it though.

lh3: can you help?

[wumblehoots]

Actaully, more information on the use of * in the read column is given here:

http://samtools.sourceforge.net/samtools.shtml

In the section corresponding the pileup option:
"Similarly, a pattern ‘-[0-9]+[ACGTNacgtn]+’ represents a deletion from the reference. The deleted bases will be presented as ‘*’ in the following lines."

[Hena]

Yes, following lines. But the question is about this line not following. Following line will have '*' in third column.