SUM_MS field in Pindel, and unique supporting reads discrepancy
The SUM_MS field in Pindel output files is the sum of mapping qualities of the anchor reads. Is this the sum of all supporting reads or just the unique reads?
Also, some lines have zero supporting unique reads, but multiple total supporting reads. Below is an example (Supporting=5, UniqueSupporting=0). How's that possible?
5416 D 6 NT 0 "" ChrID chr1 BP 195746746 195746753 BP_range 195746746 195746769 Supports 5 0 + 4 0 - 1 0 S1 10 SUM_MS 145 2 NumSupSamples 2 0 310T1 190 166 2 0 1 0 310T2 170 150 2 0 0 0
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sum of mapping quality of all supporting reads. Can you tell me the Pindel version? we have a fix in the past.
Kai
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Hi Kai. Thanks a lot for your response. I'm using version 0.2.5a3, Oct 24 2013.