Originally posted by Rui
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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.Leave a comment:
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samtools manual says they are " ’>’ or ’<’ for a reference skip".
http://samtools.sourceforge.net/samtools.shtmlLeave a comment:
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mpileup format
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.
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