I've been using the -s option of samtools "pileup" to output the mapping qualities for each read at each position as a last column in the pileup file.
I know that the "pileup" command is deprecated, and I need to switch to the "mpileup" command, but "mpileup" doesn't seem to have an option for including the map qualities. Does anyone have any advice? I know that the map quality is still reported once at the beginning of each read, but it seems like it will be tricky to map that quality to the correct base in each subsequent position. I'm hoping there's an easier alternative...
Thanks for any help!
Kris Weber
Research Assistant
Noble Lab, Department of Genome Sciences
University of Washington
I know that the "pileup" command is deprecated, and I need to switch to the "mpileup" command, but "mpileup" doesn't seem to have an option for including the map qualities. Does anyone have any advice? I know that the map quality is still reported once at the beginning of each read, but it seems like it will be tricky to map that quality to the correct base in each subsequent position. I'm hoping there's an easier alternative...
Thanks for any help!
Kris Weber
Research Assistant
Noble Lab, Department of Genome Sciences
University of Washington
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