User: volkansevim

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volkansevim10
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Posts by volkansevim

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Comment: C: Pindel Somatic Calls?
... I'm interested in your filter. How can I get it? ...
written 3.6 years ago by volkansevim10
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Pindel: direct tumor/tumor comparison
... I've got a dataset with normal and two tumor samples (from the same tumor) for each patient. Let's call those n, t1, and t2. I want to compare insertions and deletions in t1 to those in t2. Is it advisable to run Pindel using directly t1 and t2, i.e., use t1 as normal sample? The alternative is to r ...
pindel written 3.6 years ago by volkansevim10 • updated 3.4 years ago by Biostar ♦♦ 20
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Answer: A: SUM_MS field in Pindel, and unique supporting reads discrepancy
... Hi Kai. Thanks a lot for your response. I'm using version 0.2.5a3, Oct 24 2013. ...
written 3.6 years ago by volkansevim10
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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 ...
pindel written 3.6 years ago by volkansevim10
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Filtering overlapping calls in Pindel
... I'm running Pindel on some tumor/normal pairs. I noticed that the output contains some overlapping calls as shown below. Start positions of the deletions are the same, but the ends shift by 1bp. 217    D    4    NT    0        ChrID    chr1    BP    7828173    7828178    BP_range    7828173    7828 ...
indels pindel written 3.6 years ago by volkansevim10 • updated 17 months ago by Biostar ♦♦ 20

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