Question: SUM_MS field in Pindel, and unique supporting reads discrepancy
1
gravatar for volkansevim
3.5 years ago by
volkansevim10
Bay Area
volkansevim10 wrote:

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 • 810 views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by volkansevim10
2
gravatar for liangkaiye
3.5 years ago by
liangkaiye250
United States
liangkaiye250 wrote:

sum of mapping quality of all supporting reads. Can you tell me the Pindel version? we have a fix in the past.

 

Kai

ADD COMMENTlink written 3.5 years ago by liangkaiye250
0
gravatar for volkansevim
3.5 years ago by
volkansevim10
Bay Area
volkansevim10 wrote:

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

ADD COMMENTlink written 3.5 years ago by volkansevim10
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