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
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
