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Old 11-03-2010, 09:53 AM   #1
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Default 2 pileup format questions

In the samtools documentation on pileup format, it states
A pattern `\+[0-9]+[ACGTNacgtn]+' indicates there is an insertion between this reference position and the next reference position. The length of the insertion is given by the integer in the pattern, followed by the inserted sequence. Here is an example of 2bp insertions on three reads:
seq2 156 A 11 .$......+2AG.+2AG.+2AGGG <975;:<<<<<
Similarly, a pattern `-[0-9]+[ACGTNacgtn]+' represents a deletion from the reference. Here is an exmaple of a 4bp deletions from the reference, supported by two reads:
seq3 200 A 20 ,,,,,..,.-4CACC.-4CACC....,.,,.^~. ==<<<<<<<<<<<::<;2<<
I'm trying to implement a filter on pileup lines & I'm unclear whether insert or deletions have an effect on the quality string. I'm guessing that insert operations have the quality value of the first base of the insert in the quality string, but wanted to double check that.

Also, what do > and < mean in a pileup sequence line (line below was generated by samtools)?

chr10   53746655        A       15      ><>>>..+1CC...GG^L.^~.  (&:/"P`"R`T````
thanks in advance
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Old 11-03-2010, 10:52 AM   #2
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in the latest online document. >< denote "reference skip", depending on the strand. they are added in samtools-0.1.9. quality corresponding to indels actually means nothing. ignore them.
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