SUM_MS field in Pindel, and unique supporting reads discrepancy
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8.4 years ago
volvox ▴ 40

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
pindel • 1.9k views
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Hi Kai. Thanks a lot for your response. I'm using version 0.2.5a3, Oct 24 2013.

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8.4 years ago
liangkaiye ▴ 250

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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