mpileup format

[hanleng]

I am using samtools mpileup to analyze my data, and have several lines like this:

chr1 14976 G 5 <<><> HHHHH
chr1 14977 C 5 <<><> HHHHH
chr1 14978 C 5 <<><> HHHHH
chr1 14979 T 5 <<><> HHHHH
chr1 14980 C 5 <<><> HHHHH
chr1 14981 A 5 <<><> HHHHH
chr1 14982 T 5 <<><> HHHHH
chr1 14983 G 5 <<><> HHHHH
chr1 14984 A 5 <<><> HHHHH


What are those ">" "<" or "*" mean in the reads base column? According to the description of the format (http://samtools.sourceforge.net/pileup.shtml), they should be only in the base qualities columns.

[rnaseek]

samtools manual says they are " ’>’ or ’<’ for a reference skip".

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

[hanleng]

samtools manual says they are " ’>’ or ’<’ for a reference skip".

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

Thank u! This is really helpful!

[Rui]

I am sorry to kick this thread alive but did someone figure out what "*" means in the reads base column? I cannot find any information on the homepage of Samtools.

[Yvone]

I am sorry to kick this thread alive but did someone figure out what "*" means in the reads base column? I cannot find any information on the homepage of Samtools.

The deleted bases will be presented as ‘*’ in the following lines.