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Old 05-14-2013, 06:53 AM   #1
volavii
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Location: GERMANY

Join Date: Apr 2013
Posts: 16
Default samtools mpileup

Hey guys,

i`m new to the field of ngs and have a question regarding the mpileup option -M:
-M INT cap mapping quality at INT [60]

i dont get the need of this option.
Why is it necessary to cap a mapping quality of 60? Its in my opinion a good value...
And what is ment by cap? Does this means, that this read is totally ignored becaus its mapping quality is exactly 60?! I have realy no clue of the consequence of this option.
So without mentioning this option each read having a mapping quality of 60 is ignored? :/

i hope someone can help me out here...

oh still one question:)
is there anywhere a detailed description of the ALL parameters?
the manual http://samtools.sourceforge.net/samtools.shtml seems to exmplain only a part of all parameters in detail...


Many thanks in advance:)

volavii
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