Question: Filtering overlapping calls in Pindel
gravatar for volkansevim
4.8 years ago by
Bay Area
volkansevim10 wrote:

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    7828192
218    D    5    NT    0        ChrID    chr1    BP    7828173    7828179    BP_range    7828173    7828192
219    D    6    NT    0        ChrID    chr1    BP    7828173    7828180    BP_range    7828173    7828192
220    D    7    NT    0        ChrID    chr1    BP    7828173    7828181    BP_range    7828173    7828192

How would you pick one? Is it reasonable to use the SUM_MS per supported read?


pindel indels • 1.4k views
ADD COMMENTlink modified 2.7 years ago by Biostar ♦♦ 20 • written 4.8 years ago by volkansevim10
gravatar for liangkaiye
4.8 years ago by
United States
liangkaiye250 wrote:

this is a homopolymer region so that we would probably see all possible alleles if you sequence ultra deep. If this sample is MSI, have you tried our recent MSIsensor This tool approaches the variant detection differently. 

ADD COMMENTlink written 4.8 years ago by liangkaiye250
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