Question: Filtering overlapping calls in Pindel
0
gravatar for volkansevim
3.4 years ago by
volkansevim10
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?

Thanks.

pindel indels • 1.0k views
ADD COMMENTlink modified 16 months ago by Biostar ♦♦ 20 • written 3.4 years ago by volkansevim10
1
gravatar for liangkaiye
3.4 years ago by
liangkaiye250
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 http://bioinformatics.oxfordjournals.org/content/early/2013/12/24/bioinformatics.btt755? This tool approaches the variant detection differently. 

ADD COMMENTlink written 3.4 years ago by liangkaiye250
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